Methods and compositions for treating a proprotein convertase subtilisin kexin (pcsk9) gene-associated disorder

ABSTRACT

The invention relates to methods of inhibiting the expression of a PCSK9 gene in a subject, as well as therapeutic and prophylactic methods for treating subjects having a lipid disorder, such as a hyperlipidemia using RNAi agents, e.g., double-stranded RNAi agents, targeting the PCSK9 gene.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.16/929,470, filed on Jul. 15, 2020, which is a continuation of U.S.patent application Ser. No. 16/744,689, filed on Jan. 16, 2020, now U.S.Pat. No. 10,851,377, issued on Dec. 1, 2020, which is a continuation ofU.S. patent application Ser. No. 15/895,023, filed on Feb. 13, 2018,abandoned, which is a 35 § U.S.C. 111(a) continuation application whichclaims the benefit of priority to PCT/US2016/048666, filed on Aug. 25,2016, which claims the benefit of priority to U.S. Provisional PatentApplication No. 62/209,526, filed on Aug. 25, 2015. The entire contentsof each of the foregoing patent applications are incorporated herein byreference.

This application is related to U.S. Provisional Application No.61/733,518, filed on Dec. 5, 2012; U.S. Provisional Application No.61/793,530, filed on Mar. 15, 2013; U.S. Provisional Application No.61/886,916, filed on Oct. 4, 2013; U.S. Provisional Application No.61/892,188, filed on Oct. 17, 2013; PCT Application No.PCT/US2013/073349, filed on Dec. 5, 2013; U.S. patent application Ser.No. 14/650,128, filed on Jun. 5, 2015, now U.S. Pat. No. 10,125,369,issued on Nov. 13, 2018, and U.S. patent application Ser. No.16/155,965, filed on Oct. 10, 2018. The entire contents of each of theforegoing patent applications are hereby incorporated herein byreference.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Mar. 29, 2022, isnamed 121301_04406_SL.txt and is 188,345 bytes in size.

BACKGROUND OF THE INVENTION

Proprotein convertase subtilisin kexin 9 (PCSK9) is a member of thesubtilisin serine protease family. The other eight mammalian subtilisinproteases, PCSK1-PCSK8 (also called PC1/3, PC2, furin, PC4, PC5/6,PACE4, PC7, and S1P/SKI-1) are proprotein convertases that process awide variety of proteins in the secretory pathway and play roles indiverse biological processes (Bergeron, F. (2000) J. Mol. Endocrinol.24, 1-22, Gensberg, K., (1998) Semin. Cell Dev. Biol. 9, 11-17, Seidah,N. G. (1999) Brain Res. 848, 45-62, Taylor, N. A., (2003) FASEB J. 17,1215-1227, and Zhou, A., (1999) J. Biol. Chem. 274, 20745-20748).

PCSK9 has been proposed to play a role in cholesterol metabolism. PCSK9mRNA expression is down-regulated by dietary cholesterol feeding in mice(Maxwell, K. N., (2003) J. Lipid Res. 44, 2109-2119), up-regulated bystatins in HepG2 cells (Dubuc, G., (2004) Arterioscler. Thromb. Vasc.Biol. 24, 1454-1459), and up-regulated in sterol regulatory elementbinding protein (SREBP) transgenic mice (Horton, J. D., (2003) Proc.Natl. Acad. Sci. USA 100, 12027-12032), similar to the cholesterolbiosynthetic enzymes and the low-density lipoprotein receptor (LDLR).Furthermore, PCSK9 missense mutations have been found to be associatedwith a form of autosomal dominant hypercholesterolemia (Hchola3)(Abifadel, M., et al. (2003) Nat. Genet. 34, 154-156, Timms, K. M.,(2004) Hum. Genet. 114, 349-353, Leren, T. P. (2004) Clin. Genet. 65,419-422). PCSK9 may also play a role in determining LDL cholesterollevels in the general population, because single-nucleotidepolymorphisms (SNPs) have been associated with cholesterol levels in aJapanese population (Shioji, K., (2004) J. Hum. Genet. 49, 109-114).

Autosomal dominant hypercholesterolemias (ADHs) are monogenic diseasesin which patients exhibit elevated total and LDL cholesterol levels,tendon xanthomas, and premature atherosclerosis (Rader, D. J., (2003) J.Clin. Invest. 111, 1795-1803). The pathogenesis of ADHs and a recessiveform, autosomal recessive hypercholesterolemia (ARH) (Cohen, J. C.,(2003) Curr. Opin. Lipidol. 14, 121-127), is due to defects in LDLuptake by the liver. ADH may be caused by LDLR mutations, which preventLDL uptake, or by mutations in the protein on LDL, apolipoprotein B,which binds to the LDLR. ARH is caused by mutations in the ARH proteinthat are necessary for endocytosis of the LDLR-LDL complex via itsinteraction with clathrin. Therefore, if PCSK9 mutations are causativein Hchola3 families, it seems likely that PCSK9 plays a role inreceptor-mediated LDL uptake.

Overexpression studies point to a role for PCSK9 in controlling LDLRlevels and, hence, LDL uptake by the liver (Maxwell, K. N. (2004) Proc.Natl. Acad. Sci. USA 101, 7100-7105, Benjannet, S., et al. (2004) J.Biol. Chem. 279, 48865-48875, Park, S. W., (2004) J. Biol. Chem. 279,50630-50638). Adenoviral-mediated overexpression of mouse or human PCSK9for 3 or 4 days in mice results in elevated total and LDL cholesterollevels; this effect is not seen in LDLR knockout animals (Maxwell, K. N.(2004) Proc. Natl. Acad. Sci. USA 101, 7100-7105, Benjannet, S., et al.(2004) J. Biol. Chem. 279, 48865-48875, Park, S. W., (2004) J. Biol.Chem. 279, 50630-50638). In addition, PCSK9 overexpression results in asevere reduction in hepatic LDLR protein, without affecting LDLR mRNAlevels, SREBP protein levels, or SREBP protein nuclear to cytoplasmicratio.

While hypercholesterolemia itself is asymptomatic, longstandingelevation of serum cholesterol can lead to atherosclerosis. Over aperiod of decades, chronically elevated serum cholesterol contributes toformation of atheromatous plaques in the arteries which can lead toprogressive stenosis or even complete occlusion of the involvedarteries. In addition, smaller plaques may rupture and cause a clot toform and obstruct blood flow resulting in, for example, myocardialinfarction and/or stroke. If the formation of the stenosis or occlusionis gradual, blood supply to the tissues and organs slowly diminishesuntil organ function becomes impaired.

Accordingly, there is a need in the art for effective treatments forPCSK9-associated diseases, such as a hyperlipidemia, e.g.,hypercholesterolemia.

SUMMARY OF THE INVENTION

The present invention is based, at least in part, on the surprisingdiscovery that a single dose of a double-stranded RNAi agent comprisingchemical modifications shows an exceptional potency and durability toinhibit expression of PCSK9. Specifically, a single fixed dose, e.g., afixed dose of about 300 mg to about 500 mg, of RNAi agents targeting ahuman PCSK9 gene, e.g., nucleotides 3544-3623 of a human PCSK9 gene(nucleotides 3544-3623 of SEQ ID NO:1), e.g., nucleotides 3601-3623 ofSEQ ID NO:1, including a GalNAc ligand are shown herein to beexceptionally effective and durable in silencing the activity of a PCSK9gene.

Accordingly, the present invention provides methods for inhibitingexpression of a PCSK9 gene in a subject and methods for treating asubject having a disorder that would benefit from inhibiting or reducingthe expression of a PCSK9 gene, e.g., a disorder mediated by PCSK9expression, such as a hyperlipidemia, e.g., hypercholesterolemia, usingiRNA compositions which effect the RNA-induced silencing complex(RISC)-mediated cleavage of RNA transcripts of a PCSK9 gene.

In one aspect, the methods of the present invention for inhibitingexpression of a PCSK9 gene in a subject and methods for treating asubject having a disorder that would benefit from inhibiting or reducingthe expression of a PCSK9 gene, e.g., a disorder mediated by PCSK9expression, such as a hyperlipidemia, e.g., hypercholesterolemia,include administering to a subject a fixed dose of about 25 mg to about800 mg of a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the sense strandcomprises at least 15 contiguous nucleotides differing by no more than 3nucleotides from the nucleotide sequence of SEQ ID NO:1 and theantisense strand comprises at least 15 contiguous nucleotides differingby no more than 3 nucleotides from the nucleotide sequence of SEQ IDNO:2, wherein substantially all of the nucleotides of the sense strandand substantially all of the nucleotides of the antisense strand aremodified nucleotides, and wherein the sense strand is conjugated to aligand attached at the 3′-terminus.

In one aspect, the present invention provides methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods include comprisingadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby inhibitingthe expression of the PCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject, comprisingadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby decreasingthe level of LDLc in the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression. The methods include administering to the subject a fixeddose of about 25 mg to about 800 mg of a double-stranded ribonucleicacid (RNAi) agent, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,the antisense strand comprising a region of complementarity whichcomprises at least 15 contiguous nucleotides differing by no more than 3nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQID NO:1 thereby treating the subject having a disorder that wouldbenefit from reduction in PCSK9 expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby treatingthe subject having hpercholesterolemia.

The fixed dose may administered to the subject at an interval of once aweek, once every two weeks, once a month, once a quarter, or bianually.

In one embodiment, the subject is administered a fixed dose of about 25mg to about 50 mg once a week. In another embodiment, the subject isadministered a fixed dose of about 50 mg to about 100 mg once every twoweeks. In another embodiment, the subject is administered a fixed doseof about 100 mg to about 200 mg once a month. In yet another embodiment,the subject is administered a fixed dose of about 300 mg to about 800 mgonce a quarter. In another embodiment, the subject is administered afixed dose of about 300 mg to about 800 mg biannually.

The present invention also provides methods in which the RNAi agent isadministered in a dosing regimen that includes a loading phase and amaintenance phase.

Accordingly, in one aspect, the present invention provides methods ofinhibiting the expression of a PCSK9 gene in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering a fixed dose of about 200 mg to about 600 mg of the RNAiagent to the subject, and wherein the maintenance phase comprisesadministering a fixed dose of about 25 mg to about 100 mg of the RNAiagent to the subject about once a month, wherein the double-strandedRNAi agent comprises a sense strand and an antisense strand forming adouble stranded region, the antisense strand comprising a region ofcomplementarity which comprises at least 15 contiguous nucleotidesdiffering by no more than 3 nucleotides from nucleotides 3544-3623 ofthe nucleotide sequence of SEQ ID NO:1, thereby inhibiting theexpression of the PCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering to the subject a fixed dose of about 200 mg to about 600mg of the RNAi agent, and wherein the maintenance phase comprisesadministering to the subject a fixed dose of about 25 mg to about 100 mgof the RNAi agent once a month, wherein the double-stranded RNAi agentcomprises a sense strand and an antisense strand forming a doublestranded region, the antisense strand comprising a region ofcomplementarity which comprises at least 15 contiguous nucleotidesdiffering by no more than 3 nucleotides from nucleotides 3544-3623 ofthe nucleotide sequence of SEQ ID NO:1, thereby decreasing the level ofLDLc in the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression. The methods include administering to the subject adouble-stranded ribonucleic acid (RNAi) agent in a dosing regimen thatincludes a loading phase followed by a maintenance phase, wherein theloading phase comprises administering to the subject a fixed dose ofabout 200 mg to about 600 mg of the RNAi agent, and wherein themaintenance phase comprises administering to the subject a fixed dose ofabout 25 mg to about 100 mg of the RNAi agent once a month, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby treatingthe subject having a disorder that would benefit from reduction in PCSK9expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering tothe subject a fixed dose of about 200 mg to about 600 mg of the RNAiagent, and wherein the maintenance phase comprises administering to thesubject a fixed dose of about 25 mg to about 100 mg of the RNAi agentonce a month, wherein the double-stranded RNAi agent comprises a sensestrand and an antisense strand forming a double stranded region, theantisense strand comprising a region of complementarity which comprisesat least 15 contiguous nucleotides differing by no more than 3nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQID NO:1, thereby treating the subject having hyperlipidemia.

The double stranded RNAi agent may be administered to the subjectsubcutaneously, e.g., by subcutaneous injection, or intramuscularly.

In one embodiment, the antisense strand comprises a nucleotide sequenceselected from the group consisting of any one of the unmodifiednucleotide sequences provided in Table 1. In one embodiment, thedouble-stranded RNAi agent targets nucleotides 3601-3623 of SEQ ID NO:1.In one embodiment, the agent targeting nucleotides 3601-3623 of SEQ IDNO:1 is AD-60212.

In one embodiment, the antisense strand comprises the nucleotidesequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685).

In one embodiment, the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686).

In one embodiment, the double-stranded ribonucleic acid RNAi agentcomprises at least one modified nucleotide.

In one embodiment, substantially of the nucleotides of the sense strandare modified nucleotides. In another embodiment, substantially all ofthe nucleotides of the antisense strand are modified nucleotides. In yetanother embodiment, substantially of the nucleotides of the sense strandand substantially all of the nucleotides of the antisense strand aremodified nucleotides.

In one embodiment, all of the nucleotides of the sense strand aremodified nucleotides. In another embodiment, all of the nucleotides ofthe antisense strand are modified nucleotides. In yet anotherembodiment, all of the nucleotides of the sense strand and all of thenucleotides of the antisense strand are modified nucleotides.

In one aspect, the present invention provides methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods includeadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, therebyinhibiting expression of the PCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a fixed dose of about 25 mg toabout 800 mg of a double-stranded ribonucleic acid (RNAi) agent, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, therebydecreasing the level of LDLc in the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression, comprising administering to the subject a fixed dose ofabout 25 mg to about 800 mg of a double-stranded ribonucleic acid (RNAi)agent, wherein the double-stranded RNAi agent comprises a sense strandand an antisense strand forming a double stranded region, wherein theantisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides, thereby treating the subject having a disorderthat would benefit from reduction in PCSK9 expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, therebytreating the subject having hyperlipidemia.

In one aspect, the present invention provides methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods includeadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, andadministering to the subject a therapeutically effective amount of ananti-PCSK9 antibody, or antigen-binding fragment thereof, therebyinhibiting expression of the PCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a fixed dose of about 25 mg toabout 800 mg of a double-stranded ribonucleic acid (RNAi) agent, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, andadministering to the subject a therapeutically effective amount of ananti-PCSK9 antibody, or antigen-binding fragment thereof, therebydecreasing the level of LDLc in the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression, comprising administering to the subject a fixed dose ofabout 25 mg to about 800 mg of a double-stranded ribonucleic acid (RNAi)agent, wherein the double-stranded RNAi agent comprises a sense strandand an antisense strand forming a double stranded region, wherein theantisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′(SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby treating the subject having adisorder that would benefit from reduction in PCSK9 expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, andadministering to the subject a therapeutically effective amount of ananti-PCSK9 antibody, or antigen-binding fragment thereof, therebytreating the subject having hyperlipidemia.

The fixed dose may administered to the subject at an interval of once aweek, once every two weeks, once a month, once a quarter, or bianually.

In one embodiment, the subject is administered a fixed dose of about 25mg to about 50 mg once a week. In another embodiment, the subject isadministered a fixed dose of about 50 mg to about 100 mg once every twoweeks. In another embodiment, the subject is administered a fixed doseof about 100 mg to about 200 mg once a month. In yet another embodiment,the subject is administered a fixed dose of about 300 mg to about 800 mgonce a quarter. In another embodiment, the subject is administered afixed dose of about 300 mg to about 800 mg biannually.

In one aspect, the present invention provide methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering afixed dose of about 200 mg to about 600 mg of the RNAi agent to thesubject, and wherein the maintenance phase comprises administering tothe subject a fixed dose of about 25 mg to about 100 mg of the RNAiagent once a quarter, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,wherein the antisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides, thereby inhibiting expression of the PCSK9gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering a fixed dose of about 200 mg to about 600 mg of the RNAiagent to the subject, and wherein the maintenance phase comprisesadministering to the subject a fixed dose of about 25 mg to about 100 mgof the RNAi agent once a quarter, wherein the double-stranded RNAi agentcomprises a sense strand and an antisense strand forming a doublestranded region, wherein the antisense strand comprises the nucleotidesequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sensestrand comprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′(SEQ ID NO: 686), wherein substantially all of the nucleotides of thesense strand and substantially all of the nucleotides of the antisensestrand are modified nucleotides, thereby decreasing the level of LDLc inthe subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression. The methods include administering to the subject adouble-stranded ribonucleic acid (RNAi) agent in a dosing regimen thatincludes a loading phase followed by a maintenance phase, wherein theloading phase comprises administering a fixed dose of about 200 mg toabout 600 mg of the RNAi agent to the subject, and wherein themaintenance phase comprises administering to the subject a fixed dose ofabout 25 mg to about 100 mg of the RNAi agent once a quarter, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, therebytreating the subject having a disorder that would benefit from reductionin PCSK9 expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering afixed dose of about 200 mg to about 600 mg of the RNAi agent to thesubject, and wherein the maintenance phase comprises administering tothe subject a fixed dose of about 25 mg to about 100 mg of the RNAiagent once a quarter, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,wherein the antisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides, thereby treating the subject havinghyperlipidemia.

In one aspect, the present invention provide methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering afixed dose of about 200 mg to about 600 mg of the RNAi agent to thesubject, and wherein the maintenance phase comprises administering tothe subject a fixed dose of about 25 mg to about 100 mg of the RNAiagent once a quarter, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,wherein the antisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby inhibiting expression of thePCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering a fixed dose of about 200 mg to about 600 mg of the RNAiagent to the subject, and wherein the maintenance phase comprisesadministering to the subject a fixed dose of about 25 mg to about 100 mgof the RNAi agent once a quarter, wherein the double-stranded RNAi agentcomprises a sense strand and an antisense strand forming a doublestranded region, wherein the antisense strand comprises the nucleotidesequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sensestrand comprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′(SEQ ID NO: 686), wherein substantially all of the nucleotides of thesense strand and substantially all of the nucleotides of the antisensestrand are modified nucleotides, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby decreasing the level of LDLcin the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression. The methods include administering to the subject adouble-stranded ribonucleic acid (RNAi) agent in a dosing regimen thatincludes a loading phase followed by a maintenance phase, wherein theloading phase comprises administering a fixed dose of about 200 mg toabout 600 mg of the RNAi agent to the subject, and wherein themaintenance phase comprises administering to the subject a fixed dose ofabout 25 mg to about 100 mg of the RNAi agent once a quarter, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the antisense strandcomprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ IDNO: 685) and the sense strand comprises the nucleotide sequence5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686), wherein substantially allof the nucleotides of the sense strand and substantially all of thenucleotides of the antisense strand are modified nucleotides, andadministering to the subject a therapeutically effective amount of ananti-PCSK9 antibody, or antigen-binding fragment thereof, therebytreating the subject having a disorder that would benefit from reductionin PCSK9 expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering afixed dose of about 200 mg to about 600 mg of the RNAi agent to thesubject, and wherein the maintenance phase comprises administering tothe subject a fixed dose of about 25 mg to about 100 mg of the RNAiagent once a quarter, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,wherein the antisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby treating the subject havinghyperlipidemia.

In one embodiment, the subject is a human.

In one embodiment, the disorder that would benefit from reduction inPCSK9 expression is hyperlipidemia, such as hypercholesterolemia.

In one embodiment, the hyperlipidemia is hypercholesterolemia.

The double stranded RNAi agent may be administered to the subjectsubcutaneously, e.g., by subcutaneous injection, or intramuscularly.

In one embodiment, the sense strand comprises the nucleotide sequence of5′-csusagacCfuGfudTuugcuuuugu-3′ (SEQ ID NO: 687) and the antisensestrand comprises the nucleotide sequence of5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688) (AD-60212),wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, or U; Af, Gf, Cfor Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine; and s is aphosphorothioate linkage.

In one embodiment, the double-stranded ribonucleic acid RNAi agentfurther comprises a ligand.

In one embodiment, the ligand is conjugated to the 3′ end of the sensestrand of the double-stranded ribonucleic acid RNAi agent.

In one embodiment, the ligand is an N-acetylgalactosamine (GalNAc)derivative.

In one embodiment, the ligand is

In one embodiment, the double-stranded ribonucleic acid RNAi agent isconjugated to the ligand as shown in the following schematic

and, wherein X is O or S. In one embodiment, the X is O.

In one embodiment, PCSK9 expression is inhibited by at least about 30%.

In one embodiment, the methods of the invention further comprisedetermining an LDLR genotype or phenotype of the subject.

In one embodiment, administering the double-stranded RNAi agent resultsin a decrease in serum cholesterol in the subject and/or a decrease inPCSK9 protein accumulation.

In one embodiment, the methods of the invention further comprisedetermining the serum cholesterol level in the subject.

In one embodiment, the methods of the invention further comprisecomprising administering an additional therapeutic agent to the subject,e.g., a statin and/or an anti-PCSK9 antibody. In one embodiment, theanti-PCSK9 antibody is selected from the group consisting of alirocumab(Praluent), evolocumab (Repatha), and bococizumab.

In one embodiment, the RNAi agent is administered as a pharmaceuticalcomposition.

The RNAi agent may be administered in an unbuffered solution, such assaline or water, or administered with a buffer solution. In oneembodiment, the buffer solution comprises acetate, citrate, prolamine,carbonate, or phosphate or any combination thereof. In anotherembodiment, the buffer solution is phosphate buffered saline (PBS).

In one aspect, the present invention provides methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods includeadministering to the subject a single fixed dose of about 25 mg to about800 mg of a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the sense strandcomprises the nucleotide sequence of 5′-csusagacCfuGfudTuugcuuuugu-3′(SEQ ID NO: 687) and the antisense strand comprises the nucleotidesequence of 5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688)(AD-60212), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, orU; Af, Gf, Cf or Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine;and s is a phosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby inhibiting expression of thePCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a fixed dose of about 25 mg toabout 800 mg of a double-stranded ribonucleic acid (RNAi) agent, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the sense strandcomprises the nucleotide sequence of 5′-csusagacCfuGfudTuugcuuuugu-3′(SEQ ID NO: 687) and the antisense strand comprises the nucleotidesequence of 5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688)(AD-60212), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, orU; Af, Gf, Cf or Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine;and s is a phosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby decreasing the level of LDLcin the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression. The methods include administering to the subject a fixeddose of about 25 mg to about 800 mg of a double-stranded ribonucleicacid (RNAi) agent, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,wherein the sense strand comprises the nucleotide sequence of5′-csusagacCfuGfudTuugcuuuugu-3′ (SEQ ID NO: 687) and the antisensestrand comprises the nucleotide sequence of5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688) (AD-60212),wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, or U; Af, Gf, Cfor Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine; and s is aphosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby treating the subject having adisorder that would benefit from reduction in PCSK9 expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a fixed dose of about 25 mg to about 800 mgof a double-stranded ribonucleic acid (RNAi) agent, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the sense strandcomprises the nucleotide sequence of 5′-csusagacCfuGfudTuugcuuuugu-3′(SEQ ID NO: 687) and the antisense strand comprises the nucleotidesequence of 5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688)(AD-60212), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, orU; Af, Gf, Cf or Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine;and s is a phosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby treating the subject havinghyperlipidemia.

In one embodiment, the subject is administered a fixed dose of about 200mg to about 800 mg once a quarter. In another embodiment, the subject isadministered a fixed dose of about 200 mg to about 800 mg biannually.

In one aspect, the present invention provides methods of inhibiting theexpression of a PCSK9 gene in a subject. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering afixed dose of about 200 mg to about 600 mg of the RNAi agent to thesubject, and wherein the maintenance phase comprises administering tothe subject a fixed dose of about 25 mg to about 800 mg of the RNAiagent once a quarter, wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,wherein the sense strand comprises the nucleotide sequence of5′-csusagacCfuGfudTuugcuuuugu-3′ (SEQ ID NO: 687) and the antisensestrand comprises the nucleotide sequence of5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688) (AD-60212),wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, or U; Af, Gf, Cfor Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine; and s is aphosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby inhibiting expression of thePCSK9 gene in the subject.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering a fixed dose of about 200 mg to about 600 mg of the RNAiagent to the subject, and wherein the maintenance phase comprisesadministering to the subject a fixed dose of about 25 mg to about 100 mgof the RNAi agent once a quarter, wherein the double-stranded RNAi agentcomprises a sense strand and an antisense strand forming a doublestranded region, wherein the sense strand comprises the nucleotidesequence of 5′-csusagacCfuGfudTuugcuuuugu-3′ (SEQ ID NO: 687) and theantisense strand comprises the nucleotide sequence of5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688) (AD-60212),wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, or U; Af, Gf, Cfor Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine; and s is aphosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby decreasing the level of LDLcin the subject.

In yet another aspect, the present invention provides methods oftreating a subject having a disorder that would benefit from reductionin PCSK9 expression. The methods include administering to the subject adouble-stranded ribonucleic acid (RNAi) agent in a dosing regimen thatincludes a loading phase followed by a maintenance phase, wherein theloading phase comprises administering a fixed dose of about 200 mg toabout 600 mg of the RNAi agent to the subject, and wherein themaintenance phase comprises administering to the subject a fixed dose ofabout 25 mg to about 100 mg of the RNAi agent once a quarter, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the sense strandcomprises the nucleotide sequence of 5′-csusagacCfuGfudTuugcuuuugu-3′(SEQ ID NO: 687) and the antisense strand comprises the nucleotidesequence of 5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688)(AD-60212), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, orU; Af, Gf, Cf or Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine;and s is a phosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby treating the subject having adisorder that would benefit from reduction in PCSK9 expression.

In another aspect, the present invention provides methods of treating asubject having hyperlipidemia. The methods include administering to thesubject a double-stranded ribonucleic acid (RNAi) agent in a dosingregimen that includes a loading phase followed by a maintenance phase,wherein the loading phase comprises administering a fixed dose of about200 mg to about 600 mg of the RNAi agent to the subject, and wherein themaintenance phase comprises administering to the subject a fixed dose ofabout 25 mg to about 100 mg of the RNAi agent once a quarter, whereinthe double-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, wherein the sense strandcomprises the nucleotide sequence of 5′-csusagacCfuGfudTuugcuuuugu-3′(SEQ ID NO: 687) and the antisense strand comprises the nucleotidesequence of 5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688)(AD-60212), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, orU; Af, Gf, Cf or Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine;and s is a phosphorothioate linkage, and administering to the subject atherapeutically effective amount of an anti-PCSK9 antibody, orantigen-binding fragment thereof, thereby treating the subject havinghyperlipidemia.

In one embodiment, the subject is administered the maintenance does as afixed dose of about 200 mg to about 800 mg once a quarter. In anotherembodiment, the subject is administered the maintenance does as a fixeddose of about 200 mg to about 800 mg biannually.

In one embodiment, the double-stranded ribonucleic acid RNAi agentfurther comprises a ligand.

In one embodiment, the ligand is conjugated to the 3′ end of the sensestrand of the double-stranded ribonucleic acid RNAi agent.

In one embodiment, the ligand is an N-acetylgalactosamine (GalNAc)derivative.

In one embodiment, the ligand is

In one embodiment, the double-stranded ribonucleic acid RNAi agent isconjugated to the ligand as shown in the following schematic

and, wherein X is O or S. In one embodiment, the X is O.

In one embodiment, the anti-PCSK9 antibody, or antigen-binding fragmentthereof, is selected from the group consisting of alirocumab (Praluent),evolocumab (Repatha), and bococizumab.

In one embodiment, the methods further include administering anadditional therapeutic agent, e.g., a statin, to the subject.

In one aspect, the present invention provides kits for performing themethod of the invention. The kits include the RNAi agent, andinstructions for use, and optionally, means for administering the RNAiagent to the subject.

The present invention is further illustrated by the following detaileddescription and drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph showing the knockdown of PCSK9 protein levels, shownas a percent mean PCSK9 knockdown relative to baseline, in subjectsreceiving a single fixed dose of AD-60212.

FIG. 2 is a graph showing the lowering of LDL-c levels, shown as apercent mean LCL-C lowering relative to baseline, in subjects receivinga single fixed dose of AD-60212.

FIG. 3 is a graph showing the knockdown of PCSK9 protein levels, shownas a percent mean PCSK9 knockdown relative to baseline, in subjectsreceiving multiple fixed doses of AD-60212.

FIG. 4 is a graph showing the lowering of LDL-c levels, shown as apercent mean LCL-C lowering relative to baseline, in subjects receivingmultiple fixed doses of AD-60212.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based, at least in part, on the surprisingdiscovery that a single dose of a double-stranded RNAi agent comprisingchemical modifications shows an exceptional potency and durability toinhibit expression of PCSK9. Specifically, a single fixed dose, e.g., afixed dose of about 300 mg to about 500 mg, of RNAi agents targeting ahuman PCSK9 gene, e.g., nucleotides 3544-3623 of a human PCSK9 gene(nucleotides 3544-3623 of SEQ ID NO:1), e.g., nucleotides 3601-3623 ofSEQ ID NO:1, including a GalNAc ligand are shown herein to beexceptionally effective and durable in silencing the activity of a PCSK9gene.

Accordingly, the present invention provides methods for inhibitingexpression of a PCSK9 gene and methods for treating a subject having adisorder that would benefit from inhibiting or reducing the expressionof a PCSK9 gene, e.g., a disorder mediated by PCSK9 expression, such asa hyperlipidemia, e.g., hypercholesterolemia, using iRNA compositionswhich effect the RNA-induced silencing complex (RISC)-mediated cleavageof RNA transcripts of a PCSK9 gene.

The following detailed description discloses how to make and usecompositions containing iRNAs to inhibit the expression of a PCSK9 gene,as well as compositions, uses, and methods for treating subjects havingdiseases and disorders that would benefit from inhibition and/orreduction of the expression of this gene.

I. Definitions

In order that the present invention may be more readily understood,certain terms are first defined. In addition, it should be noted thatwhenever a value or range of values of a parameter are recited, it isintended that values and ranges intermediate to the recited values arealso intended to be part of this invention.

The articles “a” and “an” are used herein to refer to one or to morethan one (i.e., to at least one) of the grammatical object of thearticle. By way of example, “an element” means one element or more thanone element, e.g., a plurality of elements.

The term “including” is used herein to mean, and is used interchangeablywith, the phrase “including but not limited to”.

The term “or” is used herein to mean, and is used interchangeably with,the term “and/or,” unless context clearly indicates otherwise. Forexample, “sense strand or antisense strand” is understood as “sensestrand or antisense strand or sense strand and antisense strand.”

The term “about” is used herein to mean within the typical ranges oftolerances in the art. For example, “about” can be understood as about 2standard deviations from the mean. In certain embodiments, about means+10%. In certain embodiments, about means +5%. When about is presentbefore a series of numbers or a range, it is understood that “about” canmodify each of the numbers in the series or range.

The term “at least” prior to a number or series of numbers is understoodto include the number adjacent to the term “at least”, and allsubsequent numbers or integers that could logically be included, asclear from context. For example, the number of nucleotides in a nucleicacid molecule must be an integer. For example, “at least 18 nucleotidesof a 21 nucleotide nucleic acid molecule” means that 18, 19, 20, or 21nucleotides have the indicated property. When at least is present beforea series of numbers or a range, it is understood that “at least” canmodify each of the numbers in the series or range.

As used herein, “no more than” or “less than” is understood as the valueadjacent to the phrase and logical lower values or integers, as logicalfrom context, to zero. For example, a duplex with an overhang of “nomore than 2 nucleotides” has a 2, 1, or 0 nucleotide overhang. When “nomore than” is present before a series of numbers or a range, it isunderstood that “no more than” can modify each of the numbers in theseries or range.

As used herein, “PCSK9” refers to the proprotein convertase subtilisinkexin 9 gene or protein. PCSK9 is also known as FH3, HCHOLA3, NARC-1, orNARC1. The term PCSK9 includes human PCSK9, the amino acid andnucleotide sequence of which may be found in, for example, GenBankAccession No. GI:299523249 (SEQ ID NO:1); mouse PCSK9, the amino acidand nucleotide sequence of which may be found in, for example, GenBankAccession No. GI:163644257; rat PCSK9, the amino acid and nucleotidesequence of which may be found in, for example, GenBank Accession No.GI:77020249.

Additional examples of PCSK9 mRNA sequences are readily available usingpublicly available databases, e.g., GenBank, UniProt, and OMIM.

In one embodiment, the subject is a human, such as a human being treatedor assessed for a disease, disorder or condition that would benefit fromreduction in PCSK9 expression; a human at risk for a disease, disorderor condition that would benefit from reduction in PCSK9 expression; ahuman having a disease, disorder or condition that would benefit fromreduction in PCSK9 expression; and/or human being treated for a disease,disorder or condition that would benefit from reduction in PCSK9expression as described herein.

As used herein, the terms “treating” or “treatment” refer to abeneficial or desired result including, but not limited to, alleviationor amelioration of one or more symptoms associated with a disorder thatwould benefit from reduction in PCSK9 expression, or slowing orreversing the progression of such a disorder, whether detectable orundetectable. For example, in the context of hyperlipidemia, treatmentmay include a decrease in serum lipid levels, e.g., a decrease in lowdensity lipoprotein cholesterol (LDLc). “Treatment” can also meanprolonging survival as compared to expected survival in the absence oftreatment.

As used herein, “prevention” or “preventing,” when used in reference toa disease, disorder or condition thereof, that would benefit from areduction in expression of a PCSK9 gene, refers to a reduction in thelikelihood that a subject will develop a symptom associated with adisease, disorder, or condition mediated by PCSK9 expression, e.g., asymptom such as cardiovascular disease, e.g., coronary artery disease(CAD) (also known as coronary heart disease (CHD)), or transientischemic attack (TIA) or stroke. The likelihood of developing a such asymptom is reduced, for example, when an individual having one or morerisk factors (e.g., diabetes, previous personal history of CHD ornoncoronary atherosclerosis (e.g., abdominal aortic aneurysm, peripheralartery disease, and carotid artery stenosis), family history ofcardiovascular disease, e.g., in male relatives younger than 50 years orin female relatives younger than age 60 years, tobacco use,hypertension, and/or obesity (BMI ≥30)) for a disease, disorder, orcondition mediated by PCSK9 expression, e.g., hypercholesterolemia,either fails to develop, for example, coronary artery disease, ordevelops, e.g., coronary artery disease, with less severity relative toa population having the same risk factors and not receiving treatment asdescribed herein. The failure to develop a disease, disorder orcondition, or the reduction in the development of a symptom associatedwith such a disease, disorder or condition (e.g., by at least about 10%on a clinically accepted scale for that disease or disorder), or theexhibition of delayed symptoms delayed (e.g., by days, weeks, months oryears) is considered effective prevention. Prevention can requireadministration of more than one dose.

The interchangeably used terms “PCSK9-associated disease” and “disorderthat would benefit from a reduction in PCSK9 expression,” as usedherein, are intended to include any disease, disorder, or conditionassociated with the PCSK9 gene or protein. Such a disease may be caused,for example, by excess production of the PCSK9 protein, by PCSK9 genemutations, by abnormal cleavage of the PCSK9 protein, by abnormalinteractions between PCSK9 and other proteins or other endogenous orexogenous substances. Exemplary PCSK9-associated diseases includelipidemias, e.g., a hyperlipidemia, and other forms of lipid imbalancesuch as hypercholesterolemia, hypertriglyceridemia and the pathologicalconditions associated with these disorders, e.g., CHD andatherosclerosis.

As used herein the term “hypercholesterolemia” refers to a form ofhyperlipidemia (elevated levels of lipids in the blood) in which thereare high levels of cholesterol in the serum of a subject, e.g., at leastabout 240 mg/dL of total cholesterol.

As used herein, the term “cardiovascular disease” refers to a diseaseaffecting the heart or blood vessels, which includes, for example,arteriosclerosis, coronary artery disease (or narrowing of thearteries), heart valve disease, arrhythmia, heart failure, hypertension,orthostatic hypotension, shock, endocarditis, diseases of the aorta andits branches, disorders of the peripheral vascular system, heart attack,cardiomyopathy, and congenital heart disease.

“Therapeutically effective amount,” as used herein, is intended toinclude the amount of an RNAi agent that, when administered to a patientfor treating a PCSK9 associated disease, is sufficient to effecttreatment of the disease (e.g., by diminishing, ameliorating ormaintaining the existing disease or one or more symptoms of disease).The “therapeutically effective amount” may vary depending on the RNAiagent, how the agent is administered, the disease and its severity andthe history, age, weight, family history, genetic makeup, stage ofpathological processes mediated by PCSK9 expression, the types ofpreceding or concomitant treatments, if any, and other individualcharacteristics of the patient to be treated.

“Prophylactically effective amount,” as used herein, is intended toinclude the amount of an RNAi agent that, when administered to a subjectwho does not yet experience or display symptoms of a PCSK9-associateddisease, but who may be predisposed to the disease, is sufficient toprevent or ameliorate the disease or one or more symptoms of thedisease. Ameliorating the disease includes slowing the course of thedisease or reducing the severity of later-developing disease. The“prophylactically effective amount” may vary depending on the RNAiagent, how the agent is administered, the degree of risk of disease, andthe history, age, weight, family history, genetic makeup, the types ofpreceding or concomitant treatments, if any, and other individualcharacteristics of the patient to be treated.

A “therapeutically-effective amount” or “prophylactically effectiveamount” also includes an amount of an RNAi agent that produces somedesired local or systemic effect at a reasonable benefit/risk ratioapplicable to any treatment. RNAi gents employed in the methods of thepresent invention may be administered in a sufficient amount to producea reasonable benefit/risk ratio applicable to such treatment.

As used herein, “target sequence” refers to a contiguous portion of thenucleotide sequence of an mRNA molecule formed during the transcriptionof a PCSK9 gene, including mRNA that is a product of RNA processing of aprimary transcription product. In one embodiment, the target portion ofthe sequence will be at least long enough to serve as a substrate foriRNA-directed cleavage at or near that portion of the nucleotidesequence of an mRNA molecule formed during the transcription of a PCSK9gene.

The target sequence may be from about 9-36 nucleotides in length, e.g.,about 15-30 nucleotides in length. For example, the target sequence canbe from about 15-30 nucleotides, 15-29, 15-28, 15-27, 15-26, 15-25,15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29,18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30,19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20,20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24, 20-23, 20-22, 20-21,21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22nucleotides in length. In some embodiments, the target sequence is about19 to about 30 nucleotides in length. In other embodiments, the targetsequence is about 19 to about 25 nucleotides in length. In still otherembodiments, the target sequence is about 19 to about 23 nucleotides inlength. In some embodiments, the target sequence is about 21 to about 23nucleotides in length. Ranges and lengths intermediate to the aboverecited ranges and lengths are also contemplated to be part of theinvention.

As used herein, the term “strand comprising a sequence” refers to anoligonucleotide comprising a chain of nucleotides that is described bythe sequence referred to using the standard nucleotide nomenclature.

“G,” “C,” “A,” “T” and “U” each generally stand for a nucleotide thatcontains guanine, cytosine, adenine, thymidine and uracil as a base,respectively. However, it will be understood that the term“ribonucleotide” or “nucleotide” can also refer to a modifiednucleotide, as further detailed below, or a surrogate replacement moiety(see, e.g., Table B). The skilled person is well aware that guanine,cytosine, adenine, and uracil can be replaced by other moieties withoutsubstantially altering the base pairing properties of an oligonucleotidecomprising a nucleotide bearing such replacement moiety. For example,without limitation, a nucleotide comprising inosine as its base can basepair with nucleotides containing adenine, cytosine, or uracil. Hence,nucleotides containing uracil, guanine, or adenine can be replaced inthe nucleotide sequences of dsRNA featured in the invention by anucleotide containing, for example, inosine. In another example, adenineand cytosine anywhere in the oligonucleotide can be replaced withguanine and uracil, respectively to form G-U Wobble base pairing withthe target mRNA. Sequences containing such replacement moieties aresuitable for the compositions and methods featured in the invention.

The terms “iRNA”, “RNAi agent,” “iRNA agent,” “RNA interference agent”as used interchangeably herein, refer to an agent that contains RNA asthat term is defined herein, and which mediates the targeted cleavage ofan RNA transcript via an RNA-induced silencing complex (RISC) pathway.iRNA directs the sequence-specific degradation of mRNA through a processknown as RNA interference (RNAi). The iRNA modulates, e.g., inhibits,the expression of PCSK9 in a cell, e.g., a cell within a subject, suchas a mammalian subject.

In one embodiment, an RNAi agent of the invention includes a singlestranded RNA that interacts with a target RNA sequence, e.g., a PCSK9target mRNA sequence, to direct the cleavage of the target RNA. Withoutwishing to be bound by theory it is believed that long double strandedRNA introduced into cells is broken down into siRNA by a Type IIIendonuclease known as Dicer (Sharp et al. (2001) Genes Dev. 15:485).Dicer, a ribonuclease-Ill-like enzyme, processes the dsRNA into 19-23base pair short interfering RNAs with characteristic two base 3′overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs arethen incorporated into an RNA-induced silencing complex (RISC) where oneor more helicases unwind the siRNA duplex, enabling the complementaryantisense strand to guide target recognition (Nykanen, et al., (2001)Cell 107:309). Upon binding to the appropriate target mRNA, one or moreendonucleases within the RISC cleave the target to induce silencing(Elbashir, et al., (2001) Genes Dev. 15:188). Thus, in one aspect theinvention relates to a single stranded RNA (siRNA) generated within acell and which promotes the formation of a RISC complex to effectsilencing of the target gene, i.e., a PCSK9 gene. Accordingly, the term“siRNA” is also used herein to refer to an RNAi as described above.

In another embodiment, the RNAi agent may be a single-stranded siRNAthat is introduced into a cell or organism to inhibit a target mRNA.Single-stranded RNAi agents bind to the RISC endonuclease, Argonaute 2,which then cleaves the target mRNA. The single-stranded siRNAs aregenerally 15-30 nucleotides and are chemically modified. The design andtesting of single-stranded siRNAs are described in U.S. Pat. No.8,101,348 and in Lima et al., (2012) Cell 150: 883-894, the entirecontents of each of which are hereby incorporated herein by reference.Any of the antisense nucleotide sequences described herein may be usedas a single-stranded siRNA as described herein or as chemically modifiedby the methods described in Lima et al., (2012) Cell 150:883-894.

In another embodiment, an “iRNA” for use in the compositions, uses, andmethods of the invention is a double-stranded RNA and is referred toherein as a “double stranded RNAi agent,” “double-stranded RNA (dsRNA)molecule,” “dsRNA agent,” or “dsRNA”. The term “dsRNA” refers to acomplex of ribonucleic acid molecules, having a duplex structurecomprising two anti-parallel and substantially complementary nucleicacid strands, referred to as having “sense” and “antisense” orientationswith respect to a target RNA, i.e., a PCSK9 gene. In some embodiments ofthe invention, a double-stranded RNA (dsRNA) triggers the degradation ofa target RNA, e.g., an mRNA, through a post-transcriptionalgene-silencing mechanism referred to herein as RNA interference or RNAi.

In general, the majority of nucleotides of each strand of a dsRNAmolecule are ribonucleotides, but as described in detail herein, each orboth strands can also include one or more non-ribonucleotides, e.g., adeoxyribonucleotide and/or a modified nucleotide. In addition, as usedin this specification, an “RNAi agent” may include ribonucleotides withchemical modifications; an RNAi agent may include substantialmodifications at multiple nucleotides. Such modifications may includeall types of modifications disclosed herein or known in the art. Anysuch modifications, as used in a siRNA type molecule, are encompassed by“RNAi agent” for the purposes of this specification and claims.

The duplex region may be of any length that permits specific degradationof a desired target RNA through a RISC pathway, and may range from about9 to 36 base pairs in length, e.g., about 15-30 base pairs in length,for example, about 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, or 36 base pairsin length, such as about 15-30, 15-29, 15-28, 15-27, 15-26, 15-25,15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29,18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30,19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20,20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24, 20-23, 20-22, 20-21,21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 basepairs in length. Ranges and lengths intermediate to the above recitedranges and lengths are also contemplated to be part of the invention.

The two strands forming the duplex structure may be different portionsof one larger RNA molecule, or they may be separate RNA molecules. Wherethe two strands are part of one larger molecule, and therefore areconnected by an uninterrupted chain of nucleotides between the 3′-end ofone strand and the 5′-end of the respective other strand forming theduplex structure, the connecting RNA chain is referred to as a “hairpinloop.” A hairpin loop can comprise at least one unpaired nucleotide. Insome embodiments, the hairpin loop can comprise at least 2, at least 3,at least 4, at least 5, at least 6, at least 7, at least 8, at least 9,at least 10, at least 20, at least 23 or more unpaired nucleotides. Insome embodiments, the hairpin loop can be 10 or fewer nucleotides. Insome embodiments, the hairpin loop can be 8 or fewer unpairednucleotides. In some embodiments, the hairpin loop can be 4-10 unpairednucleotides. In some embodiments, the hairpin loop can be 4-8nucleotides.

Where the two substantially complementary strands of a dsRNA arecomprised by separate RNA molecules, those molecules need not, but canbe covalently connected. Where the two strands are connected covalentlyby means other than an uninterrupted chain of nucleotides between the3′-end of one strand and the 5′-end of the respective other strandforming the duplex structure, the connecting structure is referred to asa “linker.” The RNA strands may have the same or a different number ofnucleotides. The maximum number of base pairs is the number ofnucleotides in the shortest strand of the dsRNA minus any overhangs thatare present in the duplex. In addition to the duplex structure, an RNAimay comprise one or more nucleotide overhangs. In one embodiment of theRNAi agent, at least one strand comprises a 3′ overhang of at least 1nucleotide. In another embodiment, at least one strand comprises a 3′overhang of at least 2 nucleotides, e.g., 2, 3, 4, 5, 6, 7, 9, 10, 11,12, 13, 14, or 15 nucleotides. In other embodiments, at least one strandof the RNAi agent comprises a 5′ overhang of at least 1 nucleotide. Incertain embodiments, at least one strand comprises a 5′ overhang of atleast 2 nucleotides, e.g., 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, or15 nucleotides. In still other embodiments, both the 3′ and the 5′ endof one strand of the RNAi agent comprise an overhang of at least 1nucleotide.

In one embodiment, an RNAi agent of the invention is a dsRNA agent, eachstrand of which comprises 19-23 nucleotides that interacts with a targetRNA sequence, i.e., a PCSK9 target mRNA sequence. Without wishing to bebound by theory, long double stranded RNA introduced into cells isbroken down into siRNA by a Type III endonuclease known as Dicer (Sharpet al. (2001) Genes Dev. 15:485). Dicer, a ribonuclease-III-like enzyme,processes the dsRNA into 19-23 base pair short interfering RNAs withcharacteristic two base 3′ overhangs (Bernstein, et al., (2001) Nature409:363). The siRNAs are then incorporated into an RNA-induced silencingcomplex (RISC) where one or more helicases unwind the siRNA duplex,enabling the complementary antisense strand to guide target recognition(Nykanen, et al., (2001) Cell 107:309). Upon binding to the appropriatetarget mRNA, one or more endonucleases within the RISC cleave the targetto induce silencing (Elbashir, et al., (2001) Genes Dev. 15:188).

In another embodiment, an RNAi agent of the invention is a dsRNA of24-30 nucleotides that interacts with a target RNA sequence, e.g., aPCSK9 target mRNA sequence, to direct the cleavage of the target RNA.Without wishing to be bound by theory, long double stranded RNAintroduced into cells is broken down into siRNA by a Type IIIendonuclease known as Dicer (Sharp et al. (2001) Genes Dev. 15:485).Dicer, a ribonuclease-III-like enzyme, processes the dsRNA into 19-23base pair short interfering RNAs with characteristic two base 3′overhangs (Bernstein, et al., (2001) Nature 409:363). The siRNAs arethen incorporated into an RNA-induced silencing complex (RISC) where oneor more helicases unwind the siRNA duplex, enabling the complementaryantisense strand to guide target recognition (Nykanen, et al., (2001)Cell 107:309). Upon binding to the appropriate target mRNA, one or moreendonucleases within the RISC cleave the target to induce silencing(Elbashir, et al., (2001) Genes Dev. 15:188).

As used herein, the term “nucleotide overhang” refers to at least oneunpaired nucleotide that protrudes from the duplex structure of an iRNA,e.g., a dsRNA. For example, when a 3′-end of one strand of a dsRNAextends beyond the 5′-end of the other strand, or vice versa, there is anucleotide overhang. A dsRNA can comprise an overhang of at least onenucleotide; alternatively the overhang can comprise at least twonucleotides, at least three nucleotides, at least four nucleotides, atleast five nucleotides or more. A nucleotide overhang can comprise orconsist of a nucleotide/nucleoside analog, including adeoxynucleotide/nucleoside. The overhang(s) can be on the sense strand,the antisense strand or any combination thereof. Furthermore, thenucleotide(s) of an overhang can be present on the 5′-end, 3′-end orboth ends of either an antisense or sense strand of a dsRNA.

In one embodiment of the dsRNA, at least one strand comprises a 3′overhang of at least 1 nucleotide. In another embodiment, at least onestrand comprises a 3′ overhang of at least 2 nucleotides, e.g., 2, 3, 4,5, 6, 7, 9, 10, 11, 12, 13, 14, or 15 nucleotides. In other embodiments,at least one strand of the RNAi agent comprises a 5′ overhang of atleast 1 nucleotide. In certain embodiments, at least one strandcomprises a 5′ overhang of at least 2 nucleotides, e.g., 2, 3, 4, 5, 6,7, 9, 10, 11, 12, 13, 14, or 15 nucleotides. In still other embodiments,both the 3′ and the 5′ end of one strand of the RNAi agent comprise anoverhang of at least 1 nucleotide.

In certain embodiments, the antisense strand of a dsRNA has a 1-10nucleotide, e.g., 0-3, 1-3, 2-4, 2-5, 4-10, 5-10, e.g., a 1, 2, 3, 4, 5,6, 7, 8, 9, or 10 nucleotide, overhang at the 3′-end and/or the 5′-end.In one embodiment, the sense strand of a dsRNA has a 1-10 nucleotide,e.g., a 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 nucleotide, overhang at the3′-end and/or the 5′-end. In another embodiment, one or more of thenucleotides in the overhang is replaced with a nucleoside thiophosphate.

In certain embodiments, the overhang on the sense strand or theantisense strand, or both, can include extended lengths longer than 10nucleotides, e.g., 1-30 nucleotides, 2-30 nucleotides, 10-30nucleotides, or 10-15 nucleotides in length. In certain embodiments, anextended overhang is on the sense strand of the duplex. In certainembodiments, an extended overhang is present on the 3′end of the sensestrand of the duplex. In certain embodiments, an extended overhang ispresent on the 5′end of the sense strand of the duplex. In certainembodiments, an extended overhang is on the antisense strand of theduplex. In certain embodiments, an extended overhang is present on the3′end of the antisense strand of the duplex. In certain embodiments, anextended overhang is present on the 5′end of the antisense strand of theduplex. In certain embodiments, one or more of the nucleotides in theoverhang is replaced with a nucleoside thiophosphate. In certainembodiments, the overhang includes a self-complementary portion suchthat the overhang is capable of forming a hairpin structure that isstable under physiological conditions.

“Blunt” or “blunt end” means that there are no unpaired nucleotides atthat end of the double stranded RNAi agent, i.e., no nucleotideoverhang. A “blunt ended” RNAi agent is a dsRNA that is double-strandedover its entire length, i.e., no nucleotide overhang at either end ofthe molecule. The RNAi agents of the invention include RNAi agents withnucleotide overhangs at one end (i.e., agents with one overhang and oneblunt end) or with nucleotide overhangs at both ends.

The term “antisense strand” or “guide strand” refers to the strand of aniRNA, e.g., a dsRNA, which includes a region that is substantiallycomplementary to a target sequence, e.g., a PCSK9 mRNA. As used herein,the term “region of complementarity” refers to the region on theantisense strand that is substantially complementary to a sequence, forexample a target sequence, e.g., a PCSK9 nucleotide sequence, as definedherein. Where the region of complementarity is not fully complementaryto the target sequence, the mismatches can be in the internal orterminal regions of the molecule. Generally, the most toleratedmismatches are in the terminal regions, e.g., within 5, 4, 3, 2, or 1nucleotides of the 5′- and/or 3′-terminus of the iRNA. In oneembodiment, a double stranded RNAi agent of the invention include anucleotide mismatch in the antisense strand. In another embodiment, adouble stranded RNAi agent of the invention include a nucleotidemismatch in the sense strand. In one embodiment, the nucleotide mismatchis, for example, within 5, 4, 3, 2, or 1 nucleotides from the3′-terminus of the iRNA. In another embodiment, the nucleotide mismatchis, for example, in the 3′-terminal nucleotide of the iRNA.

The term “sense strand,” or “passenger strand” as used herein, refers tothe strand of an iRNA that includes a region that is substantiallycomplementary to a region of the antisense strand as that term isdefined herein.

As used herein, the term “cleavage region” refers to a region that islocated immediately adjacent to the cleavage site. The cleavage site isthe site on the target at which cleavage occurs. In some embodiments,the cleavage region comprises three bases on either end of, andimmediately adjacent to, the cleavage site. In some embodiments, thecleavage region comprises two bases on either end of, and immediatelyadjacent to, the cleavage site. In some embodiments, the cleavage sitespecifically occurs at the site bound by nucleotides 10 and 11 of theantisense strand, and the cleavage region comprises nucleotides 11, 12and 13.

As used herein, and unless otherwise indicated, the term“complementary,” when used to describe a first nucleotide sequence inrelation to a second nucleotide sequence, refers to the ability of anoligonucleotide or polynucleotide comprising the first nucleotidesequence to hybridize and form a duplex structure under certainconditions with an oligonucleotide or polynucleotide comprising thesecond nucleotide sequence, as will be understood by the skilled person.Such conditions can, for example, be stringent conditions, wherestringent conditions can include: 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mMEDTA, 50° C. or 70° C. for 12-16 hours followed by washing (see, e.g.,“Molecular Cloning: A Laboratory Manual, Sambrook, et al. (1989) ColdSpring Harbor Laboratory Press). Other conditions, such asphysiologically relevant conditions as can be encountered inside anorganism, can apply. The skilled person will be able to determine theset of conditions most appropriate for a test of complementarity of twosequences in accordance with the ultimate application of the hybridizednucleotides.

Complementary sequences within an iRNA, e.g., within a dsRNA asdescribed herein, include base-pairing of the oligonucleotide orpolynucleotide comprising a first nucleotide sequence to anoligonucleotide or polynucleotide comprising a second nucleotidesequence over the entire length of one or both nucleotide sequences.Such sequences can be referred to as “fully complementary” with respectto each other herein. However, where a first sequence is referred to as“substantially complementary” with respect to a second sequence herein,the two sequences can be fully complementary, or they can form one ormore, but generally not more than 5, 4, 3 or 2 mismatched base pairsupon hybridization for a duplex up to 30 base pairs, while retaining theability to hybridize under the conditions most relevant to theirultimate application, e.g., inhibition of gene expression via a RISCpathway. However, where two oligonucleotides are designed to form, uponhybridization, one or more single stranded overhangs, such overhangsshall not be regarded as mismatches with regard to the determination ofcomplementarity. For example, a dsRNA comprising one oligonucleotide 21nucleotides in length and another oligonucleotide 23 nucleotides inlength, wherein the longer oligonucleotide comprises a sequence of 21nucleotides that is fully complementary to the shorter oligonucleotide,can yet be referred to as “fully complementary” for the purposesdescribed herein.

“Complementary” sequences, as used herein, can also include, or beformed entirely from, non-Watson-Crick base pairs and/or base pairsformed from non-natural and modified nucleotides, in so far as the aboverequirements with respect to their ability to hybridize are fulfilled.Such non-Watson-Crick base pairs include, but are not limited to, G:UWobble or Hoogstein base pairing.

The terms “complementary,” “fully complementary” and “substantiallycomplementary” herein can be used with respect to the base matchingbetween the sense strand and the antisense strand of a dsRNA, or betweenthe antisense strand of an iRNA agent and a target sequence, as will beunderstood from the context of their use.

As used herein, a polynucleotide that is “substantially complementary toat least part of” a messenger RNA (mRNA) refers to a polynucleotide thatis substantially complementary to a contiguous portion of the mRNA ofinterest (e.g., an mRNA encoding PCSK9). For example, a polynucleotideis complementary to at least a part of a PCSK9 mRNA if the sequence issubstantially complementary to a non-interrupted portion of an mRNAencoding PCSK9.

In general, the majority of nucleotides of each strand areribonucleotides, but as described in detail herein, each or both strandscan also include one or more non-ribonucleotides, e.g., adeoxyribonucleotide and/or a modified nucleotide. In addition, an “iRNA”may include ribonucleotides with chemical modifications. Suchmodifications may include all types of modifications disclosed herein orknown in the art. Any such modifications, as used in an iRNA molecule,are encompassed by “iRNA” for the purposes of this specification andclaims.

In one aspect of the invention, an agent for use in the methods andcompositions of the invention is a single-stranded antisense RNAmolecule that inhibits a target mRNA via an antisense inhibitionmechanism. The single-stranded antisense RNA molecule is complementaryto a sequence within the target mRNA. The single-stranded antisenseoligonucleotides can inhibit translation in a stoichiometric manner bybase pairing to the mRNA and physically obstructing the translationmachinery, see Dias, N. et al., (2002) Mol Cancer Ther 1:347-355. Thesingle-stranded antisense RNA molecule may be about 15 to about 30nucleotides in length and have a sequence that is complementary to atarget sequence. For example, the single-stranded antisense RNA moleculemay comprise a sequence that is at least about 15, 16, 17, 18, 19, 20,or more contiguous nucleotides from any one of the antisense sequencesdescribed herein.

II. Methods of the Invention

The present invention provides methods of inhibiting the expression of aProprotein Convertase Subtilisin Kexin 9 (PCSK9) gene in a subject. Thepresent invention also provides therapeutic and prophylactic methods fortreating or preventing diseases and conditions that can be modulated bydown regulating PCSK9 gene expression. For example, the compositionsdescribed herein can be used to treat lipidemia, e.g., a hyperlipidemiaand other forms of lipid imbalance such as hypercholesterolemia,hypertriglyceridemia and the pathological conditions associated withthese disorders such as heart and circulatory diseases. Other diseasesand conditions that can be modulated by down regulating PCSK9 geneexpression include lysosomal storage diseases including, but not limitedto, Niemann-Pick disease, Tay-Sachs disease, Lysosomal acid lipasedeficiency, and Gaucher Disease. The methods include administering tothe subject a therapeutically effective amount or prophylacticallyeffective amount of an RNAi agent of the invention. In some embodiments,the method includes administering an effective amount of a PCSK9 iRNAagent to a patient having a heterozygous LDLR genotype.

As PCSK9 regulates the levels of the LDL receptor, which in turn removescholesterol-rich LDL particles from the plasma, the effect of thedecreased expression of a PCSK9 gene preferably results in a decrease inLDLc (low density lipoprotein cholesterol) levels in the blood, and moreparticularly in the serum, of the mammal. In some embodiments, LDLclevels are decreased by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%,70%, 80%, 90% or more, as compared to pretreatment levels. Accordingly,the present invention also provides methods for lowering the level oflow density cholesterol (LDLc) in the serum of a subject.

In certain embodiments of the invention, the double-stranded RNAi agentis administered to a subject as a fixed dose. A “fixed dose” (e.g., adose in mg) means that one dose of an iRNA agent is used for allsubjects regardless of any specific subject-related factors, such asweight. In other embodiments, an iRNA agent of the invention isadministered to a subject as a weight-based dose. A “weight-based dose”(e.g., a dose in mg/kg) is a dose of the iRNA agent that will changedepending on the subject's weight.

In certain embodiments of an RNAi agent is administered to the subjectas a fixed dose of about 100 mg to about 700 mg, about 150 mg to about700 mg, about 200 mg to about 700 mg, about 250 mg to about 700 mg,about 300 mg to about 700 mg, about 350 mg to about 700 mg, about 400 mgto about 700 mg, about 450 mg to about 700 mg, about 500 mg to about 700mg, about 550 mg to about 700 mg, about 600 to about 700 mg, about 650to about 700 mg, about 100 mg to about 650 mg, about 150 mg to about 650mg, about 200 mg to about 650 mg, about 250 mg to about 650 mg, about300 mg to about 650 mg, about 350 mg to about 650 mg, about 400 mg toabout 650 mg, about 450 mg to about 650 mg, about 500 mg to about 650mg, about 550 mg to about 650 mg, about 600 to about 650 mg, about 100mg to about 600 mg, about 150 mg to about 600 mg, about 200 mg to about600 mg, about 250 mg to about 600 mg, about 300 mg to about 600 mg,about 350 mg to about 600 mg, about 400 mg to about 600 mg, about 450 mgto about 600 mg, about 500 mg to about 600 mg, about 550 mg to about 600mg, about 100 mg to about 550 mg, about 150 mg to about 550 mg, about200 mg to about 550 mg, about 250 mg to about 550 mg, about 300 mg toabout 550 mg, about 350 mg to about 550 mg, about 400 mg to about 550mg, about 450 mg to about 550 mg, about 500 mg to about 550 mg, about100 mg to about 500 mg, about 150 mg to about 500 mg, about 200 mg toabout 500 mg, about 250 mg to about 500 mg, about 300 mg to about 500mg, about 350 mg to about 500 mg, about 400 mg to about 500 mg, or about450 mg to about 500 mg, e.g., a fixed dose of about 100 mg, about 125mg, about 150 mg, about 175 mg, 200 mg, about 225 mg, about 250 mg,about 275 mg, about 300 mg, about 325 mg, about 350 mg, about 375 mg,about 400 mg, about 425 mg, about 450 mg, about 475 mg, about 500 mg,about 525 mg, about 550 mg, about 575 mg, about 600 mg, about 625 mg,about 650 mg, about 675 mg, or about 700 mg. Values and rangesintermediate to the foregoing recited values are also intended to bepart of this invention.

The administration may be repeated, for example, on a regular basis. Forexample, the fixed dose may administered to the subject at an intervalof once a week, once every two weeks, once a month, once a quarter, orbianually for six months or a year or longer, i.e., chronicadministration.

In one embodiment, the subject is administered a fixed dose of about 25mg to about 50 mg once a week. In another embodiment, the subject isadministered a fixed dose of about 50 mg to about 100 mg once every twoweeks. In another embodiment, the subject is administered a fixed doseof about 100 mg to about 200 mg once a month. In yet another embodiment,the subject is administered a fixed dose of about 300 mg to about 600 mgonce a quarter. In another embodiment, the subject is administered afixed dose of about 300 mg to about 600 mg biannually (i.e., twice ayear).

Accordingly, in one aspect, the present invention provides methods ofinhibiting the expression of a PCSK9 gene in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent, e.g., a dsRNA, of the invention (e.g., a pharmaceuticalcomposition comprising a dsRNA of the invention), wherein a total ofabout 200 mg to about 600 mg of the double-stranded RNAi agent isadministered to the subject every quarter or biannually, and wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1.

In another aspect, the present invention provides methods of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent, wherein a total of about 200 mg to about 600 mg of thedouble-stranded RNAi agent is administered to the subject every quarteror biannually, and wherein the double-stranded RNAi agent comprises asense strand and an antisense strand forming a double stranded region,the antisense strand comprising a region of complementarity whichcomprises at least 15 contiguous nucleotides differing by no more than 3nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQID NO:1, thereby decreasing the level of LDLc in the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression, such as a hyperlipidemia, e.g., hypercholesterolemia. Themethods include administering to the subject a double-strandedribonucleic acid (RNAi) agent, e.g., a dsRNA, of the invention (e.g., apharmaceutical composition comprising a dsRNA of the invention), whereina total of about 200 mg to about 600 mg of the double-stranded RNAiagent is administered to the subject every quarter or biannually, andwherein the double-stranded RNAi agent comprises a sense strand and anantisense strand forming a double stranded region, the antisense strandcomprising a region of complementarity which comprises at least 15contiguous nucleotides differing by no more than 3 nucleotides fromnucleotides 3544-3623 of the nucleotide sequence of SEQ ID NO:1. In yetanother aspect, the present invention provides methods of treating asubject having hyperlipidemia, such as hypercholestrolemia. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent, e.g., a dsRNA, of the invention (e.g., a pharmaceuticalcomposition comprising a dsRNA of the invention), wherein a total ofabout 200 mg to about 600 mg of the double-stranded RNAi agent isadministered to the subject every quarter or biannually, and wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1.

As indicated above, the administration of the RNAi agents to a subjectmay be repeated on a regular basis, for example, at an interval of oncea week, once every two weeks, once a month, once a quarter, orbianually.

Accordingly, in some embodiments, the RNAi agent is administered in adosing regimen that includes a “loading phase” of closely spacedadministrations that may be followed by a “maintenance phase”, in whichthe RNAi agent is administered at longer spaced intervals. For example,after administration weekly or biweekly for one month, administrationcan be repeated once per month, for six months or a year or longer,i.e., chronic administration.

In one embodiment, the loading phase comprises a single administrationof the RNAi agent during the first week. In another embodiment, theloading phase comprises a single administration of the RNAi agent duringthe first two weeks. In yet another embodiment, the loading phasecomprises a single administration of the RNAi agent during the firstmonth.

In certain embodiments of an RNAi agent is administered to the subjectduring a loading phase as a fixed dose of about 100 mg to about 700 mg,about 150 mg to about 700 mg, about 200 mg to about 700 mg, about 250 mgto about 700 mg, about 300 mg to about 700 mg, about 350 mg to about 700mg, about 400 mg to about 700 mg, about 450 mg to about 700 mg, about500 mg to about 700 mg, about 550 mg to about 700 mg, about 600 to about700 mg, about 650 to about 700 mg, about 100 mg to about 650 mg, about150 mg to about 650 mg, about 200 mg to about 650 mg, about 250 mg toabout 650 mg, about 300 mg to about 650 mg, about 350 mg to about 650mg, about 400 mg to about 650 mg, about 450 mg to about 650 mg, about500 mg to about 650 mg, about 550 mg to about 650 mg, about 600 to about650 mg, about 100 mg to about 600 mg, about 150 mg to about 600 mg,about 200 mg to about 600 mg, about 250 mg to about 600 mg, about 300 mgto about 600 mg, about 350 mg to about 600 mg, about 400 mg to about 600mg, about 450 mg to about 600 mg, about 500 mg to about 600 mg, about550 mg to about 600 mg, about 100 mg to about 550 mg, about 150 mg toabout 550 mg, about 200 mg to about 550 mg, about 250 mg to about 550mg, about 300 mg to about 550 mg, about 350 mg to about 550 mg, about400 mg to about 550 mg, about 450 mg to about 550 mg, about 500 mg toabout 550 mg, about 100 mg to about 500 mg, about 150 mg to about 500mg, about 200 mg to about 500 mg, about 250 mg to about 500 mg, about300 mg to about 500 mg, about 350 mg to about 500 mg, about 400 mg toabout 500 mg, or about 450 mg to about 500 mg, e.g., a fixed dose ofabout 100 mg, about 125 mg, about 150 mg, about 175 mg, 200 mg, about225 mg, about 250 mg, about 275 mg, about 300 mg, about 325 mg, about350 mg, about 375 mg, about 400 mg, about 425 mg, about 450 mg, about475 mg, about 500 mg, about 525 mg, about 550 mg, about 575 mg, about600 mg, about 625 mg, about 650 mg, about 675 mg, or about 700 mg.Values and ranges intermediate to the foregoing recited values are alsointended to be part of this invention.

In one embodiment, the maintenance phase comprises administration of adose of the RNAi agent to the subject once a month, once every twomonths, once every three months, once every four months, once every fivemonths, or once every six months. In one particular embodiment, themaintenance dose is administered to the subject once a month.

The maintenance dose or doses can be the same or lower than the initialdose, e.g., one-half of the initial dose. For example, a maintenancedose may be about 25 mg to about 100 mg administered to the subjectmonthly, for example about 25 mg to about 75 mg, about 25 mg to about 50mg, or about 50 mg to about 75 mg, e.g., about 25 mg, about 30 mg, about35 mg, about 40 mg, about 45 mg, about 50 mg, about 55 mg, about 60 mg,about 65 mg, about 70 mg, about 75 mg, about 80 mg, about 85 mg, about90 mg, about 95 mg, or about 100 mg. Values and ranges intermediate tothe foregoing recited values are also intended to be part of thisinvention.

Any of these schedules may optionally be repeated for one or moreiterations. The number of iterations may depend on the achievement of adesired effect, e.g., the suppression of a PCSK9 gene, and/or theachievement of a therapeutic or prophylactic effect, e.g., reducingserum cholesterol levels or reducing a symptom of hypercholesterolemia.Following treatment, the patient can be monitored for changes in his/hercondition. The dosage of the RNAi agent may either be increased in theevent the patient does not respond significantly to current dosagelevels, or the dose may be decreased if an alleviation of the symptomsof the disease state is observed, if the disease state has been ablated,or if undesired side-effects are observed.

Accordingly, in one aspect, the present invention provides methods ofinhibiting the expression of a PCSK9 gene in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering a fixed dose of about 200 mg to about 600 mg of the RNAiagent to the subject, and wherein the maintenance phase comprisesadministering a fixed dose of about 25 mg to about 100 mg of the RNAiagent to the subject about once a month, wherein the double-strandedRNAi agent comprises a sense strand and an antisense strand forming adouble stranded region, the antisense strand comprising a region ofcomplementarity which comprises at least 15 contiguous nucleotidesdiffering by no more than 3 nucleotides from nucleotides 3544-3623 ofthe nucleotide sequence of SEQ ID NO:1, thereby inhibiting theexpression of the PCSK9 gene in the subject.

In another aspect, the present invention provides method s of decreasingthe level of low density lipoprotein (LDLc) in a subject. The methodsinclude administering to the subject a double-stranded ribonucleic acid(RNAi) agent in a dosing regimen that includes a loading phase followedby a maintenance phase, wherein the loading phase comprisesadministering to the subject a fixed dose of about 200 mg to about 600mg of the RNAi agent, and wherein the maintenance phase comprisesadministering to the subject a fixed dose of about 25 mg to about 100 mgof the RNAi agent once a month, wherein the double-stranded RNAi agentcomprises a sense strand and an antisense strand forming a doublestranded region, the antisense strand comprising a region ofcomplementarity which comprises at least 15 contiguous nucleotidesdiffering by no more than 3 nucleotides from nucleotides 3544-3623 ofthe nucleotide sequence of SEQ ID NO:1, thereby decreasing the level ofLDLc in the subject.

In another aspect, the present invention provides methods of treating asubject having a disorder that would benefit from reduction in PCSK9expression. The methods include administering to the subject adouble-stranded ribonucleic acid (RNAi) agent in a dosing regimen thatincludes a loading phase followed by a maintenance phase, wherein theloading phase comprises administering to the subject a fixed dose ofabout 200 mg to about 600 mg of the RNAi agent, and wherein themaintenance phase comprises administering to the subject a fixed dose ofabout 25 mg to about 100 mg of the RNAi agent once a month, wherein thedouble-stranded RNAi agent comprises a sense strand and an antisensestrand forming a double stranded region, the antisense strand comprisinga region of complementarity which comprises at least 15 contiguousnucleotides differing by no more than 3 nucleotides from nucleotides3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby treatingthe subject having a disorder that would benefit from reduction in PCSK9expression.

In yet another aspect, the present invention provides methods oftreating a subject having hyperlipidemia. The methods includeadministering to the subject a double-stranded ribonucleic acid (RNAi)agent in a dosing regimen that includes a loading phase followed by amaintenance phase, wherein the loading phase comprises administering tothe subject a fixed dose of about 200 mg to about 600 mg of the RNAiagent, and wherein the maintenance phase comprises administering to thesubject a fixed dose of about 25 mg to about 100 mg of the RNAi agentonce a month, wherein the double-stranded RNAi agent comprises a sensestrand and an antisense strand forming a double stranded region, theantisense strand comprising a region of complementarity which comprisesat least 15 contiguous nucleotides differing by no more than 3nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQID NO:1, thereby treating the subject having hyperlipidemia.

In one embodiment, the double-stranded ribonucleic acid (RNAi) agent foruse in the methods of the present invention comprises a sense strand andan antisense strand forming a double stranded region, wherein theantisense strand comprises the nucleotide sequence5′-ACAAAAGCAAAACAGGUCUAGAA-3′ (SEQ ID NO: 685) and the sense strandcomprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ IDNO: 686), wherein substantially all of the nucleotides of the sensestrand and substantially all of the nucleotides of the antisense strandare modified nucleotides.

As used herein, a “subject” includes a human or non-human animal,preferably a vertebrate, and more preferably a mammal. A subject mayinclude a transgenic organism. Most preferably, the subject is a human,such as a human suffering from or predisposed to developing aPCSK9-associated disease.

The methods and uses of the invention include administering acomposition described herein such that expression of the target PCSK9gene is decreased, for an extended period of time, such as, for about 80days, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96,97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111,112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125,126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139,140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153,154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167,168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, or about 180days, or longer.

Reduction in gene expression can be assessed by any methods known in theart. For example, a reduction in the expression of PCSK9 may bedetermined by determining the mRNA expression level of PCSK9 usingmethods routine to one of ordinary skill in the art, e.g., Northernblotting, qRT-PCR, by determining the protein level of PCSK9 usingmethods routine to one of ordinary skill in the art, such as Westernblotting, immunological techniques, and/or by determining a biologicalactivity of PCSK9, such as the effect on one or more serum lipidparameters, such as, for example, total cholesterol levels, high densitylipoprotein cholesterol (HDL) levels, non-HDL levels, very low densitylipoprotein cholesterol (VLDL) levels, triglyceride levels, Lp(a)levels, and lipoprotein particle size.

Administration of the dsRNA according to the methods and uses of theinvention may result in a reduction of the severity, signs, symptoms,and/or markers of such diseases or disorders in a patient with adisorder that would benefit from reduction in PCSK9 expression. By“reduction” in this context is meant a statistically significantdecrease in such level. The reduction can be, for example, at leastabout 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%,70%, 75%, 80%, 85%, 90%, 95%, or about 100%.

Efficacy of treatment or prevention of disease can be assessed, forexample by measuring disease progression, disease remission, symptomseverity, serum lipid levels (e.g., LDLc levels), quality of life, doseof a medication required to sustain a treatment effect, level of adisease marker or any other measurable parameter appropriate for a givendisease being treated or targeted for prevention. It is well within theability of one skilled in the art to monitor efficacy of treatment orprevention by measuring any one of such parameters, or any combinationof parameters. For example, efficacy of treatment of a hyperlipidemiamay be assessed, for example, by periodic monitoring of LDLc levels.Comparisons of the later readings with the initial readings provide aphysician an indication of whether the treatment is effective. It iswell within the ability of one skilled in the art to monitor efficacy oftreatment or prevention by measuring any one of such parameters, or anycombination of parameters.

A treatment or preventive effect is evident when there is astatistically significant improvement in one or more parameters ofdisease status, or by a failure to worsen or to develop symptoms wherethey would otherwise be anticipated. As an example, a favorable changeof at least 10% in a measurable parameter of disease, and preferably atleast 20%, 30%, 40%, 50% or more can be indicative of effectivetreatment. Efficacy for a given iRNA drug or formulation of that drugcan also be judged using an experimental animal model for the givendisease as known in the art. When using an experimental animal model,efficacy of treatment is evidenced when a statistically significantreduction in a marker or symptom is observed.

Alternatively, the efficacy can be measured by a reduction in theseverity of disease as determined by one skilled in the art of diagnosisbased on a clinically accepted disease severity grading scale. Anypositive change resulting in e.g., lessening of severity of diseasemeasured using the appropriate scale, represents adequate treatmentusing an iRNA or iRNA formulation as described herein.

In general, the iRNA agent does not activate the immune system, e.g., itdoes not increase cytokine levels, such as TNF-alpha or IFN-alphalevels. For example, when measured by an assay, such as an in vitro PBMCassay, such as described herein, the increase in levels of TNF-alpha orIFN-alpha, is less than 30%, 20%, or 10% of control cells treated with acontrol dsRNA, such as a dsRNA that does not target PCSK9.

In another embodiment, administration can be provided when Low DensityLipoprotein cholesterol (LDLc) levels reach or surpass a predeterminedminimal level, such as greater than 70 mg/dL, 130 mg/dL, 150 mg/dL, 200mg/dL, 300 mg/dL, or 400 mg/dL.

The effect of the decreased PCSK9 gene preferably results in a decreasein LDLc (low density lipoprotein cholesterol) levels in the blood, andmore particularly in the serum, of the mammal. In some embodiments, LDLclevels are decreased by at least 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%,70%, 80%, 90% or more, as compared to pretreatment levels.

In some embodiments of the methods of the invention, PCSK9 expression isdecreased for an extended duration, e.g., at least one week, two weeks,three weeks, or four weeks or longer. For example, in certain instances,expression of the PCSK9 gene is suppressed by at least about 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, or 50% by administration of an iRNAagent described herein. In some embodiments, the PCSK9 gene issuppressed by at least about 60%, 70%, or 80% by administration of theiRNA agent. In some embodiments, the PCSK9 gene is suppressed by atleast about 85%, 90%, or 95% by administration of the double-strandedoligonucleotide.

The RNAi agents of the invention may be administered to a subject usingany mode of administration known in the art, including, but not limitedto subcutaneous, intravenous, intramuscular, intraocular,intrabronchial, intrapleural, intraperitoneal, intraarterial, lymphatic,cerebrospinal, and any combinations thereof. In preferred embodiments,the agents are administered subcutaneously.

In some embodiments, the administration is via a depot injection. Adepot injection may release the RNAi agent in a consistent way over aprolonged time period. Thus, a depot injection may reduce the frequencyof dosing needed to obtain a desired effect, e.g., a desired inhibitionof PCSK9, or a therapeutic or prophylactic effect. A depot injection mayalso provide more consistent serum concentrations. Depot injections mayinclude subcutaneous injections or intramuscular injections. Inpreferred embodiments, the depot injection is a subcutaneous injection.

In some embodiments, the administration is via a pump. The pump may bean external pump or a surgically implanted pump. In certain embodiments,the pump is a subcutaneously implanted osmotic pump. In otherembodiments, the pump is an infusion pump. An infusion pump may be usedfor intravenous, subcutaneous, arterial, or epidural infusions. Inpreferred embodiments, the infusion pump is a subcutaneous infusionpump. In other embodiments, the pump is a surgically implanted pump thatdelivers the RNAi agent to the liver.

Other modes of administration include epidural, intracerebral,intracerebroventricular, nasal administration, intraarterial,intracardiac, intraosseous infusion, intrathecal, and intravitreal, andpulmonary. The mode of administration may be chosen based upon whetherlocal or systemic treatment is desired and based upon the area to betreated. The route and site of administration may be chosen to enhancetargeting.

The iRNA can be administered by intravenous infusion over a period oftime, such as over a 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, or about a 25 minute period. The administrationmay be repeated, for example, on a regular basis, such as weekly,biweekly (i.e., every two weeks) for one month, two months, threemonths, four months or longer. After an initial treatment regimen, thetreatments can be administered on a less frequent basis. For example,after administration weekly or biweekly for three months, administrationcan be repeated once per month, for six months or a year or longer.

Administration of the iRNA can reduce PCSK9 levels, e.g., in a cell,tissue, blood, urine or other compartment of the patient by at leastabout 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%,19%, 20%, 21%, 22%, 23%, 24%, 25%, 26%, 27%, 28%, 29%, 30%, 31%, 32%,33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41%, 42%, 43%, 44%, 45%, 46%,47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%,61%, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, 74%,75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or at least about 99%or more.

Before administration of a full dose of the iRNA, patients can beadministered a smaller dose, such as a 5% infusion, and monitored foradverse effects, such as an allergic reaction. In another example, thepatient can be monitored for unwanted immunostimulatory effects, such asincreased cytokine (e.g., TNF-alpha or INF-alpha) levels.

Owing to the inhibitory effects on PCSK9 expression, a compositionaccording to the invention or a pharmaceutical composition preparedtherefrom can enhance the quality of life. An iRNA of the invention maybe administered in “naked” form, or as a “free iRNA.” A naked iRNA isadministered in the absence of a pharmaceutical composition. The nakediRNA may be in a suitable buffer solution. The buffer solution maycomprise acetate, citrate, prolamine, carbonate, or phosphate, or anycombination thereof. In one embodiment, the buffer solution is phosphatebuffered saline (PBS). The pH and osmolarity of the buffer solutioncontaining the iRNA can be adjusted such that it is suitable foradministering to a subject.

Alternatively, an iRNA of the invention may be administered as apharmaceutical composition, such as a dsRNA liposomal formulation.

The invention further provides methods and uses for the use of an iRNAor a pharmaceutical composition thereof, e.g., for treating a subjectthat would benefit from reduction and/or inhibition of PCSK9 expression,e.g., a subject having hyperlipidemia, e.g., hypercholesterolemia, incombination with other pharmaceuticals and/or other therapeutic methods,e.g., with known pharmaceuticals and/or known therapeutic methods, suchas, for example, those which are currently employed for treating thesedisorders. The siRNA and an additional therapeutic agent can beadministered in combination in the same composition, e.g., parenterally,or the additional therapeutic agent can be administered as part of aseparate composition or by another method described herein.

Examples of additional therapeutic agents include those known to treatan agent known to treat a lipid disorders, such as hypercholesterolemia,atherosclerosis or dyslipidemia. For example, a siRNA featured in theinvention can be administered with, e.g., an HMG-CoA reductase inhibitor(e.g., a statin), a fibrate, a bile acid sequestrant, niacin, anantiplatelet agent, an angiotensin converting enzyme inhibitor, anangiotensin II receptor antagonist (e.g., losartan potassium, such asMerck & Co.'s Cozaar®), an acylCoA cholesterol acetyltransferase (ACAT)inhibitor, a cholesterol absorption inhibitor, a cholesterol estertransfer protein (CETP) inhibitor, a microsomal triglyceride transferprotein (MTTP) inhibitor, a cholesterol modulator, a bile acidmodulator, a peroxisome proliferation activated receptor (PPAR) agonist,a gene-based therapy, a composite vascular protectant (e.g., AGI-1067,from Atherogenics), a glycoprotein IIb/IIIa inhibitor, aspirin or anaspirin-like compound, an IBAT inhibitor (e.g., S-8921, from Shionogi),a squalene synthase inhibitor, or a monocyte chemoattractant protein(MCP)-I inhibitor. Exemplary HMG-CoA reductase inhibitors includeatorvastatin (Pfizer's Lipitor®/Tahor/Sortis/Torvast/Cardyl),pravastatin (Bristol-Myers Squibb's Pravachol, Sankyo'sMevalotin/Sanaprav), simvastatin (Merck's Zocor®/Sinvacor, BoehringerIngelheim's Denan, Banyu's Lipovas), lovastatin (Merck'sMevacor/Mevinacor, Bexal's Lovastatina, Cepa; Schwarz Pharma'sLiposcler), fluvastatin (Novartis' Lescol®/Locol/Lochol, Fujisawa'sCranoc, Solvay's Digaril), cerivastatin (Bayer'sLipobay/GlaxoSmithKline's Baycol), rosuvastatin (AstraZeneca'sCrestor®), and pitivastatin (itavastatin/risivastatin) (Nissan Chemical,Kowa Kogyo, Sankyo, and Novartis). Exemplary fibrates include, e.g.,bezafibrate (e.g., Roche's Befizal®/Cedur®/Bezalip®, Kissei's Bezatol),clofibrate (e.g., Wyeth's Atromid-S®), fenofibrate (e.g., Fournier'sLipidil/Lipantil, Abbott's Tricor®, Takeda's Lipantil, generics),gemfibrozil (e.g., Pfizer's Lopid/Lipur) and ciprofibrate(Sanofi-Synthelabo's Modalim®). Exemplary bile acid sequestrantsinclude, e.g., cholestyramine (Bristol-Myers Squibb's Questran® andQuestran Light™), colestipol (e.g., Pharmacia's Colestid), andcolesevelam (Genzyme/Sankyo's WelChol™). Exemplary niacin therapiesinclude, e.g., immediate release formulations, such as Aventis' Nicobid,Upsher-Smith's Niacor, Aventis' Nicolar, and Sanwakagaku's Perycit.Niacin extended release formulations include, e.g., Kos Pharmaceuticals'Niaspan and Upsher-Smith's SIo-Niacin. Exemplary antiplatelet agentsinclude, e.g., aspirin (e.g., Bayer's aspirin), clopidogrel(Sanofi-Synthelabo/Bristol-Myers Squibb's Plavix), and ticlopidine(e.g., Sanofi-Synthelabo's Ticlid and Daiichi's Panaldine). Otheraspirin-like compounds useful in combination with a dsRNA targetingPCSK9 include, e.g., Asacard (slow-release aspirin, by Pharmacia) andPamicogrel (Kanebo/Angelini Ricerche/CEPA). Exemplaryangiotensin-converting enzyme inhibitors include, e.g., ramipril (e.g.,Aventis' Altace) and enalapril (e.g., Merck & Co.'s Vasotec). Exemplaryacyl CoA cholesterol acetyltransferase (AC AT) inhibitors include, e.g.,avasimibe (Pfizer), eflucimibe (BioMsrieux Pierre Fabre/Eli Lilly),CS-505 (Sankyo and Kyoto), and SMP-797 (Sumito). Exemplary cholesterolabsorption inhibitors include, e.g., ezetimibe (Merck/Schering-PloughPharmaceuticals Zetia®) and Pamaqueside (Pfizer). Exemplary CETPinhibitors include, e.g., Torcetrapib (also called CP-529414, Pfizer),JTT-705 (Japan Tobacco), and CETi-I (Avant Immunotherapeutics).Exemplary microsomal triglyceride transfer protein (MTTP) inhibitorsinclude, e.g., implitapide (Bayer), R-103757 (Janssen), and CP-346086(Pfizer). Other exemplary cholesterol modulators include, e.g., NO-1886(Otsuka/TAP Pharmaceutical), CI-1027 (Pfizer), and WAY-135433(Wyeth-Ayerst).

Exemplary bile acid modulators include, e.g., HBS-107 (Hisamitsu/Banyu),Btg-511 (British Technology Group), BARI-1453 (Aventis), S-8921(Shionogi), SD-5613 (Pfizer), and AZD-7806 (AstraZeneca). Exemplaryperoxisome proliferation activated receptor (PPAR) agonists include,e.g., tesaglitazar (AZ-242) (AstraZeneca), Netoglitazone (MCC-555)(Mitsubishi/Johnson & Johnson), GW-409544 (LigandPharniaceuticals/GlaxoSmithKline), GW-501516 (LigandPharmaceuticals/GlaxoSmithKline), LY-929 (Ligand Pharmaceuticals and EliLilly), LY-465608 (Ligand Pharmaceuticals and Eli Lilly), LY-518674(Ligand Pharmaceuticals and Eli Lilly), and MK-767 (Merck and Kyorin).Exemplary gene-based therapies include, e.g., AdGWEGF 121.10 (GenVec),ApoA1 (UCB Pharma/Groupe Fournier), EG-004 (Trinam) (Ark Therapeutics),and ATP-binding cassette transporter-A1 (ABCA1) (CV Therapeutics/Incyte,Aventis, Xenon). Exemplary Glycoprotein IIb/IIIa inhibitors include,e.g., roxifiban (also called DMP754, Bristol-Myers Squibb), Gantofiban(Merck KGaA/Yamanouchi), and Cromafiban (Millennium Pharmaceuticals).Exemplary squalene synthase inhibitors include, e.g., BMS-1884941(Bristol-Myers Squibb), CP-210172 (Pfizer), CP-295697 (Pfizer),CP-294838 (Pfizer), and TAK-475 (Takeda). An exemplary MCP-I inhibitoris, e.g., RS-504393 (Roche Bioscience). The anti-atherosclerotic agentBO-653 (Chugai Pharmaceuticals), and the nicotinic acid derivativeNyclin (Yamanouchi Pharmacuticals) are also appropriate foradministering in combination with a dsRNA featured in the invention.Exemplary combination therapies suitable for administration with a dsRNAtargeting PCSK9 include, e.g., advicor (Niacin/lovastatin from KosPharmaceuticals), amlodipine/atorvastatin (Pfizer), andezetimibe/simvastatin (e.g., Vytorin® 10/10, 10/20, 10/40, and 10/80tablets by Merck/Schering-Plough Pharmaceuticals). Agents for treatinghypercholesterolemia, and suitable for administration in combinationwith a dsRNA targeting PCSK9 include, e.g., lovastatin, niacin Altoprev®Extended-Release Tablets (Andrx Labs), lovastatin Caduet® Tablets(Pfizer), amlodipine besylate, atorvastatin calcium Crestor® Tablets(AstraZeneca), rosuvastatin calcium Lescol® Capsules (Novartis),fluvastatin sodium Lescol® (Reliant, Novartis), fluvastatin sodiumLipitor® Tablets (Parke-Davis), atorvastatin calcium Lofibra® Capsules(Gate), Niaspan Extended-Release Tablets (Kos), niacin Pravachol Tablets(Bristol-Myers Squibb), pravastatin sodium TriCor® Tablets (Abbott),fenofibrate Vytorin® 10/10 Tablets (Merck/Schering-PloughPharmaceuticals), ezetimibe, simvastatin WelChol™ Tablets (Sankyo),colesevelam hydrochloride Zetia® Tablets (Schering), ezetimibe Zetia®Tablets (Merck/Schering-Plough Pharmaceuticals), and ezetimibe Zocor®Tablets (Merck).

In one embodiment, an iRNA agent is administered in combination with anezetimibe/simvastatin combination (e.g., Vytorin® (Merck/Schering-PloughPharmaceuticals)).

In another embodiment, an iRNA agent is administered in combination withan anti-PCSK9 antibody. Exemplary anti-PCSK9 antibodies for use in thecombination therapies of the invention inclue, for example, alirocumab(Praluent), evolocumab (Repatha), bococizumab (PF-04950615, RN316,RN-316, L1L3; Pfizer, Rinat), lodelcizumab (LFU720, pJG04; Novartis),ralpancizumab (RN317, PF-05335810; Pfizer, Rinat), RG7652 (MPSK3169A,YW508.20.33b; Genentech), LY3015014 (Lilly), LPD1462 (h1F11;Schering-Plough), AX1 (AX189, 1B20, 1D05; Merck & Co), ALD306 (Alder);mAbl (Boehringer), and Ig1-PA4 (Nanjing Normal U.).

In one embodiment, the iRNA agent is administered to the patient, andthen the additional therapeutic agent is administered to the patient (orvice versa). In another embodiment, the iRNA agent and the additionaltherapeutic agent are administered at the same time.

In another aspect, the invention features, a method of instructing anend user, e.g., a caregiver or a subject, on how to administer an iRNAagent described herein. The method includes, optionally, providing theend user with one or more doses of the iRNA agent, and instructing theend user to administer the iRNA agent on a regimen described herein,thereby instructing the end user.

In one aspect, the invention provides a method of treating a patient byselecting a patient on the basis that the patient is in need of LDLlowering, LDL lowering without lowering of HDL, ApoB lowering, or totalcholesterol lowering. The method includes administering to the patient asiRNA in an amount sufficient to lower the patient's LDL levels or ApoBlevels, e.g., without substantially lowering HDL levels.

Genetic predisposition plays a role in the development of target geneassociated diseases, e.g., hyperlipidemia. Therefore, a patient in needof a siRNA can be identified by taking a family history, or, forexample, screening for one or more genetic markers or variants. Examplesof genes involved in hyperlipidemia include but are not limited to,e.g., LDL receptor (LDLR), the apoliproteins (ApoA1, ApoB, ApoE, and thelike), Cholesteryl ester transfer protein (CETP), Lipoprotein lipase(LPL), hepatic lipase (LIPC), Endothelial lipase (EL),Lecithinxholesteryl acyltransferase (LCAT).

A healthcare provider, such as a doctor, nurse, or family member, cantake a family history before prescribing or administering an iRNA agentof the invention. In addition, a test may be performed to determine agenotype or phenotype. For example, a DNA test may be performed on asample from the patient, e.g., a blood sample, to identify the PCSK9genotype and/or phenotype before a PCSK9 dsRNA is administered to thepatient. In another embodiment, a test is performed to identify arelated genotype and/or phenotype, e.g., a LDLR genotype. Example ofgenetic variants with the LDLR gene can be found in the art, e.g., inthe following publications which are incorporated by reference: Costanzaet al (2005) Am J Epidemiol. 15; 161(8):714-24; Yamada et al. (2008) JMed Genet. January; 45(1):22-8, Epub 2007 Aug. 31; and Boes et al (2009)Exp. Gerontol 44: 136-160, Epub 2008 Nov. 17.

The present invention further provides methods of inhibiting expressionof a Proprotein Convertase Subtilisin Kexin 9 (PCSK9) in a cell, such asa cell within a subject, e.g., a human subject.

Accordingly, the present invention provides methods of inhibitingexpression of a PCSK9 gene in a cell. The methods include contacting acell with an RNAi agent, e.g., a double stranded RNAi agent, in anamount effective to inhibit expression of the PCSK9 gene in the cell,thereby inhibiting expression of the PCSK9 in the cell.

Contacting of a cell with a double stranded RNAi agent may be done invitro or in vivo. Contacting a cell in vivo with the RNAi agent includescontacting a cell or group of cells within a subject, e.g., a humansubject, with the RNAi agent. Combinations of in vitro and in vivomethods of contacting are also possible. Contacting may be direct orindirect, as discussed above. Furthermore, contacting a cell may beaccomplished via a targeting ligand, including any ligand describedherein or known in the art. In preferred embodiments, the targetingligand is a carbohydrate moiety, e.g., a GalNAc₃ ligand, or any otherligand that directs the RNAi agent to a site of interest, e.g., theliver of a subject.

The term “inhibiting,” as used herein, is used interchangeably with“reducing,” “silencing,” “downregulating” and other similar terms, andincludes any level of inhibition.

The phrase “inhibiting expression of a PCSK9” is intended to refer toinhibition of expression of any PCSK9 gene (such as, e.g., a mouse PCSK9gene, a rat PCSK9 gene, a monkey PCSK9 gene, or a human PCSK9 gene) aswell as variants or mutants of a PCSK9 gene. Thus, the PCSK9 gene may bea wild-type PCSK9 gene, a mutant PCSK9 gene, or a transgenic PCSK9 genein the context of a genetically manipulated cell, group of cells, ororganism.

“Inhibiting expression of a PCSK9 gene” includes any level of inhibitionof a PCSK9 gene, e.g., at least partial suppression of the expression ofa PCSK9 gene. The expression of the PCSK9 gene may be assessed based onthe level, or the change in the level, of any variable associated withPCSK9 gene expression, e.g., PCSK9 mRNA level, PCSK9 protein level, orlipid levels. This level may be assessed in an individual cell or in agroup of cells, including, for example, a sample derived from a subject.

Inhibition may be assessed by a decrease in an absolute or relativelevel of one or more variables that are associated with PCSK9 expressioncompared with a control level. The control level may be any type ofcontrol level that is utilized in the art, e.g., a pre-dose baselinelevel, or a level determined from a similar subject, cell, or samplethat is untreated or treated with a control (such as, e.g., buffer onlycontrol or inactive agent control).

In some embodiments of the methods of the invention, expression of aPCSK9 gene is inhibited by at least about 5%, at least about 10%, atleast about 15%, at least about 20%, at least about 25%, at least about30%, at least about 35%, at least about 40%, at least about 45%, atleast about 50%, at least about 55%, at least about 60%, at least about65%, at least about 70%, at least about 75%, at least about 80%, atleast about 85%, at least about 90%, at least about 91%, at least about92%, at least about 93%, at least about 94%. at least about 95%, atleast about 96%, at least about 97%, at least about 98%, or at leastabout 99%.

Inhibition of the expression of a PCSK9 gene may be manifested by areduction of the amount of mRNA expressed by a first cell or group ofcells (such cells may be present, for example, in a sample derived froma subject) in which a PCSK9 gene is transcribed and which has or havebeen treated (e.g., by contacting the cell or cells with an RNAi agentof the invention, or by administering an RNAi agent of the invention toa subject in which the cells are or were present) such that theexpression of a PCSK9 gene is inhibited, as compared to a second cell orgroup of cells substantially identical to the first cell or group ofcells but which has not or have not been so treated (control cell(s)).In preferred embodiments, the inhibition is assessed by expressing thelevel of mRNA in treated cells as a percentage of the level of mRNA incontrol cells, using the following formula:

${\frac{\left( {{mRNA}{in}{control}{cells}} \right) - \left( {{mRNA}{in}{treated}{cells}} \right)}{\left( {{mRNA}{in}{control}{cells}} \right)} \cdot 100}\%$

Alternatively, inhibition of the expression of a PCSK9 gene may beassessed in terms of a reduction of a parameter that is functionallylinked to PCSK9 gene expression, e.g., PCSK9 protein expression, such aslipid levels, cholesterol levels, e.g., LDLc levels. PCSK9 genesilencing may be determined in any cell expressing PCSK9, eitherconstitutively or by genomic engineering, and by any assay known in theart. The liver is the major site of PCSK9 expression. Other significantsites of expression include the pancreas, kidney, and intestines.

Inhibition of the expression of a PCSK9 protein may be manifested by areduction in the level of the PCSK9 protein that is expressed by a cellor group of cells (e.g., the level of protein expressed in a samplederived from a subject). As explained above for the assessment of mRNAsuppression, the inhibition of protein expression levels in a treatedcell or group of cells may similarly be expressed as a percentage of thelevel of protein in a control cell or group of cells.

A control cell or group of cells that may be used to assess theinhibition of the expression of a PCSK9 gene includes a cell or group ofcells that has not yet been contacted with an RNAi agent of theinvention. For example, the control cell or group of cells may bederived from an individual subject (e.g., a human or animal subject)prior to treatment of the subject with an RNAi agent.

The level of PCSK9 mRNA that is expressed by a cell or group of cellsmay be determined using any method known in the art for assessing mRNAexpression. In one embodiment, the level of expression of PCSK9 in asample is determined by detecting a transcribed polynucleotide, orportion thereof, e.g., mRNA of the PCSK9 gene. RNA may be extracted fromcells using RNA extraction techniques including, for example, using acidphenol/guanidine isothiocyanate extraction (RNAzol B; Biogenesis),RNeasy RNA preparation kits (Qiagen) or PAXgene (PreAnalytix,Switzerland). Typical assay formats utilizing ribonucleic acidhybridization include nuclear run-on assays, RT-PCR, RNase protectionassays (Melton et al., Nuc. Acids Res. 12:7035), Northern blotting, insitu hybridization, and microarray analysis.

In one embodiment, the level of expression of PCSK9 is determined usinga nucleic acid probe. The term “probe”, as used herein, refers to anymolecule that is capable of selectively binding to a specific PCSK9.Probes can be synthesized by one of skill in the art, or derived fromappropriate biological preparations. Probes may be specifically designedto be labeled. Examples of molecules that can be utilized as probesinclude, but are not limited to, RNA, DNA, proteins, antibodies, andorganic molecules.

Isolated mRNA can be used in hybridization or amplification assays thatinclude, but are not limited to, Southern or Northern analyses,polymerase chain reaction (PCR) analyses and probe arrays. One methodfor the determination of mRNA levels involves contacting the isolatedmRNA with a nucleic acid molecule (probe) that can hybridize to PCSK9mRNA. In one embodiment, the mRNA is immobilized on a solid surface andcontacted with a probe, for example by running the isolated mRNA on anagarose gel and transferring the mRNA from the gel to a membrane, suchas nitrocellulose. In an alternative embodiment, the probe(s) areimmobilized on a solid surface and the mRNA is contacted with theprobe(s), for example, in an Affymetrix gene chip array. A skilledartisan can readily adapt known mRNA detection methods for use indetermining the level of PCSK9 mRNA.

An alternative method for determining the level of expression of PCSK9in a sample involves the process of nucleic acid amplification and/orreverse transcriptase (to prepare cDNA) of for example mRNA in thesample, e.g., by RT-PCR (the experimental embodiment set forth inMullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany(1991) Proc. Natl. Acad. Sci. USA 88:189-193), self sustained sequencereplication (Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA87:1874-1878), transcriptional amplification system (Kwoh et al. (1989)Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi etal. (1988) Bio/Technology 6:1197), rolling circle replication (Lizardiet al., U.S. Pat. No. 5,854,033) or any other nucleic acid amplificationmethod, followed by the detection of the amplified molecules usingtechniques well known to those of skill in the art. These detectionschemes are especially useful for the detection of nucleic acidmolecules if such molecules are present in very low numbers. Inparticular aspects of the invention, the level of expression of PCSK9 isdetermined by quantitative fluorogenic RT-PCR (i.e., the TaqMan™System).

The expression levels of PCSK9 mRNA may be monitored using a membraneblot (such as used in hybridization analysis such as Northern, Southern,dot, and the like), or microwells, sample tubes, gels, beads or fibers(or any solid support comprising bound nucleic acids). See U.S. Pat.Nos. 5,770,722, 5,874,219, 5,744,305, 5,677,195 and 5,445,934, which areincorporated herein by reference. The determination of PCSK9 expressionlevel may also comprise using nucleic acid probes in solution.

In preferred embodiments, the level of mRNA expression is assessed usingbranched DNA (bDNA) assays or real time PCR (qPCR). The use of thesemethods is described and exemplified in the Examples presented herein.

The level of PCSK9 protein expression may be determined using any methodknown in the art for the measurement of protein levels. Such methodsinclude, for example, electrophoresis, capillary electrophoresis, highperformance liquid chromatography (HPLC), thin layer chromatography(TLC), hyperdiffusion chromatography, fluid or gel precipitin reactions,absorption spectroscopy, a colorimetric assays, spectrophotometricassays, flow cytometry, immunodiffusion (single or double),immunoelectrophoresis, Western blotting, radioimmunoassay (RIA),enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays,electrochemiluminescence assays, and the like.

The term “sample” as used herein refers to a collection of similarfluids, cells, or tissues isolated from a subject, as well as fluids,cells, or tissues present within a subject. Examples of biologicalfluids include blood, serum and serosal fluids, plasma, lymph, urine,cerebrospinal fluid, saliva, ocular fluids, and the like. Tissue samplesmay include samples from tissues, organs or localized regions. Forexample, samples may be derived from particular organs, parts of organs,or fluids or cells within those organs. In certain embodiments, samplesmay be derived from the liver (e.g., whole liver or certain segments ofliver or certain types of cells in the liver, such as, e.g.,hepatocytes). In preferred embodiments, a “sample derived from asubject” refers to blood or plasma drawn from the subject. In furtherembodiments, a “sample derived from a subject” refers to liver tissuederived from the subject.

In some embodiments of the methods of the invention, the RNAi agent isadministered to a subject such that the RNAi agent is delivered to aspecific site within the subject. The inhibition of expression of PCSK9may be assessed using measurements of the level or change in the levelof PCSK9 mRNA or PCSK9 protein in a sample derived from fluid or tissuefrom the specific site within the subject. In preferred embodiments, thesite is the liver. The site may also be a subsection or subgroup ofcells from any one of the aforementioned sites. The site may alsoinclude cells that express a particular type of receptor.

III. iRNAs for Use in the Methods of the Invention

Described herein are methods for the use of double-stranded RNAi agentswhich inhibit the expression of a PCSK9 gene in a cell, such as a cellwithin a subject, e.g., a mammal, such as a human having aPCSK9-associated disorder, e.g., a hyperlipidemia, e.g.,hypercholesterolemia.

Accordingly, the invention provides double-stranded RNAi agents capableof inhibiting the expression of a target gene (i.e., a PCSK9 gene) invivo for use in the claimed methods.

In one embodiment, the RNA of the iRNA of the invention e.g., a dsRNA,is un-modified, and does not comprise, e.g., chemical modificationsand/or conjugations known in the art and described herein. In anotherembodiment, the RNA of an iRNA of the invention, e.g., a dsRNA, ischemically modified to enhance stability or other beneficialcharacteristics. In certain aspects of the invention, substantially allof the nucleotides of an iRNA of the invention are modified. For examplesubstantially all of the nucleotides of the sense strand are modifiednucleotides, and/or substantially all of the nucleotides of theantisense strand are modified nucleotides and/or substantially all ofthe nucleotides of both the sense strand and the antisense strand aremodified nucleotides. In other embodiments of the invention, all of thenucleotides of an iRNA of the invention are modified. For example all ofthe nucleotides of the sense strand are modified nucleotides, and/or allof the nucleotides of the antisense strand are modified nucleotidesand/or all of the nucleotides of both the sense strand and the antisensestrand are modified nucleotides. iIRNAs of the invention in which“substantially all of the nucleotides are modified” are largely but notwholly modified and can include not more than 5, 4, 3, 2, or 1unmodified nucleotides.

The dsRNA includes an antisense strand having a region ofcomplementarity which is complementary to at least a part of an mRNAformed in the expression of a PCSK9 gene. The region of complementarityis about 30 nucleotides or less in length (e.g., about 30, 29, 28, 27,26, 25, 24, 23, 22, 21, 20, 19, or 18 nucleotides or less in length).Upon contact with a cell expressing the PCSK9 gene, the iRNA inhibitsthe expression of the PCSK9 gene (e.g., a humanPCSK9 gene) by at leastabout 10% as assayed by, for example, a PCR or branched DNA (bDNA)-basedmethod, or by a protein-based method, such as by immunofluorescenceanalysis, using, for example, Western Blotting or flowcytometrictechniques.

A dsRNA includes two RNA strands that are complementary and hybridize toform a duplex structure under conditions in which the dsRNA will beused. One strand of a dsRNA (the antisense strand) includes a region ofcomplementarity that is substantially complementary, and generally fullycomplementary, to a target sequence. The target sequence can be derivedfrom the sequence of an mRNA formed during the expression of a PCSK9gene. The other strand (the sense strand) includes a region that iscomplementary to the antisense strand, such that the two strandshybridize and form a duplex structure when combined under suitableconditions. As described elsewhere herein and as known in the art, thecomplementary sequences of a dsRNA can also be contained asself-complementary regions of a single nucleic acid molecule, as opposedto being on separate oligonucleotides.

Generally, the duplex structure is between 15 and 30 base pairs inlength, e.g., between, 15-29, 15-28, 15-27, 15-26, 15-25, 15-24, 15-23,15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30, 18-29, 18-28, 18-27,18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20, 19-30, 19-29, 19-28,19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21, 19-20, 20-30, 20-29,20-28, 20-27, 20-26, 20-25, 20-24, 20-23, 20-22, 20-21, 21-30, 21-29,21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22 base pairs in length.Ranges and lengths intermediate to the above recited ranges and lengthsare also contemplated to be part of the invention.

Similarly, the region of complementarity to the target sequence isbetween 15 and 30 nucleotides in length, e.g., between 15-29, 15-28,15-27, 15-26, 15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18,15-17, 18-30, 18-29, 18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22,18-21, 18-20, 19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23,19-22, 19-21, 19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24,20-23, 20-22, 20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24,21-23, or 21-22 nucleotides in length. Ranges and lengths intermediateto the above recited ranges and lengths are also contemplated to be partof the invention.

In some embodiments, the dsRNA is about 15 to about 20 nucleotides inlength, or between about 25 and about 30 nucleotides in length. Ingeneral, the dsRNA is long enough to serve as a substrate for the Dicerenzyme. For example, it is well-known in the art that dsRNAs longer thanabout 21-23 nucleotides in length may serve as substrates for Dicer. Asthe ordinarily skilled person will also recognize, the region of an RNAtargeted for cleavage will most often be part of a larger RNA molecule,often an mRNA molecule. Where relevant, a “part” of an mRNA target is acontiguous sequence of an mRNA target of sufficient length to allow itto be a substrate for RNAi-directed cleavage (i.e., cleavage through aRISC pathway).

In certain embodiments, a dsRNA agent of the invention may include anRNA strand (the antisense strand) which can include longer lengths, forexample up to 66 nucleotides, e.g., 36-66, 26-36, 25-36, 31-60, 22-43,27-53 nucleotides in length with a region of at least 19 contiguousnucleotides that is substantially complementary to at least a part of anmRNA transcript of a PCSK9 gene. These dsRNA agents with the longerlength antisense strands preferably include a second RNA strand (thesense strand) of 20-60 nucleotides in length wherein the sense andantisense strands form a duplex of 18-30 contiguous nucleotides.

One of skill in the art will also recognize that the duplex region is aprimary functional portion of a dsRNA, e.g., a duplex region of about 9to 36 base pairs, e.g., about 10-36, 11-36, 12-36, 13-36, 14-36, 15-36,9-35, 10-35, 11-35, 12-35, 13-35, 14-35, 15-35, 9-34, 10-34, 11-34,12-34, 13-34, 14-34, 15-34, 9-33, 10-33, 11-33, 12-33, 13-33, 14-33,15-33, 9-32, 10-32, 11-32, 12-32, 13-32, 14-32, 15-32, 9-31, 10-31,11-31, 12-31, 13-32, 14-31, 15-31, 15-30, 15-29, 15-28, 15-27, 15-26,15-25, 15-24, 15-23, 15-22, 15-21, 15-20, 15-19, 15-18, 15-17, 18-30,18-29, 18-28, 18-27, 18-26, 18-25, 18-24, 18-23, 18-22, 18-21, 18-20,19-30, 19-29, 19-28, 19-27, 19-26, 19-25, 19-24, 19-23, 19-22, 19-21,19-20, 20-30, 20-29, 20-28, 20-27, 20-26, 20-25, 20-24, 20-23, 20-22,20-21, 21-30, 21-29, 21-28, 21-27, 21-26, 21-25, 21-24, 21-23, or 21-22base pairs.

Thus, in one embodiment, to the extent that it becomes processed to afunctional duplex, of e.g., 15-30 base pairs, that targets a desired RNAfor cleavage, an RNA molecule or complex of RNA molecules having aduplex region greater than 30 base pairs is a dsRNA. Thus, an ordinarilyskilled artisan will recognize that in one embodiment, a miRNA is adsRNA. In another embodiment, a dsRNA is not a naturally occurringmiRNA. In another embodiment, an iRNA agent useful to target PCSK9expression is not generated in the target cell by cleavage of a largerdsRNA.

A dsRNA as described herein can further include one or moresingle-stranded nucleotide overhangs e.g., 1, 2, 3, or 4 nucleotides.dsRNAs having at least one nucleotide overhang can have unexpectedlysuperior inhibitory properties relative to their blunt-endedcounterparts. A nucleotide overhang can comprise or consist of anucleotide/nucleoside analog, including a deoxynucleotide/nucleoside.The overhang(s) can be on the sense strand, the antisense strand or anycombination thereof. Furthermore, the nucleotide(s) of an overhang canbe present on the 5′-end, 3′-end or both ends of either an antisense orsense strand of a dsRNA. In certain embodiments, longer, extendedoverhangs are possible.

A dsRNA can be synthesized by standard methods known in the art asfurther discussed below, e.g., by use of an automated DNA synthesizer,such as are commercially available from, for example, Biosearch, AppliedBiosystems, Inc.

iRNA compounds of the invention may be prepared using a two-stepprocedure. First, the individual strands of the double-stranded RNAmolecule are prepared separately. Then, the component strands areannealed. The individual strands of the siRNA compound can be preparedusing solution-phase or solid-phase organic synthesis or both. Organicsynthesis offers the advantage that the oligonucleotide strandscomprising unnatural or modified nucleotides can be easily prepared.Single-stranded oligonucleotides of the invention can be prepared usingsolution-phase or solid-phase organic synthesis or both.

In one aspect, a dsRNA of the invention includes at least two nucleotidesequences, a sense sequence and an anti-sense sequence. The sense strandis selected from the group of sequences provided in Table 1, and thecorresponding antisense strand of the sense strand is selected from thegroup of sequences of Table 1. In this aspect, one of the two sequencesis complementary to the other of the two sequences, with one of thesequences being substantially complementary to a sequence of an mRNAgenerated in the expression of a PCSK9 gene. As such, in this aspect, adsRNA will include two oligonucleotides, where one oligonucleotide isdescribed as the sense strand in Table 1, and the second oligonucleotideis described as the corresponding antisense strand of the sense strandin Table 1. In one embodiment, the substantially complementary sequencesof the dsRNA are contained on separate oligonucleotides. In anotherembodiment, the substantially complementary sequences of the dsRNA arecontained on a single oligonucleotide.

It will be understood that, although some of the sequences in Table 1are described as modified and/or conjugated sequences, the RNA of theiRNA of the invention e.g., a dsRNA of the invention, may comprise anyone of the sequences set forth in Table 1 that is un-modified,un-conjugated, and/or modified and/or conjugated differently thandescribed therein.

The skilled person is well aware that dsRNAs having a duplex structureof between about 20 and 23 base pairs, e.g., 21, base pairs have beenhailed as particularly effective in inducing RNA interference (Elbashiret al., EMBO 2001, 20:6877-6888). However, others have found thatshorter or longer RNA duplex structures can also be effective (Chu andRana (2007) RNA 14:1714-1719; Kim et al. (2005) Nat Biotech 23:222-226).In the embodiments described above, by virtue of the nature of theoligonucleotide sequences provided in Table 1, dsRNAs described hereincan include at least one strand of a length of minimally 21 nucleotides.It can be reasonably expected that shorter duplexes having one of thesequences of any one of Table 1 minus only a few nucleotides on one orboth ends can be similarly effective as compared to the dsRNAs describedabove. Hence, dsRNAs having a sequence of at least 15, 16, 17, 18, 19,20, or more contiguous nucleotides derived from one of the sequences ofany one of Tables 3, 4, 5, 6, 18, 19, 20, 21, and 23, and differing intheir ability to inhibit the expression of a PCSK9 gene by not more thanabout 5, 10, 15, 20, 25, or 30% inhibition from a dsRNA comprising thefull sequence, are contemplated to be within the scope of the presentinvention.

In addition, the RNAs provided in Table 1 identify a site(s) in a PCSK9transcript that is susceptible to RISC-mediated cleavage. As such, thepresent invention further features iRNAs that target within one of thesesites. As used herein, an iRNA is said to target within a particularsite of an RNA transcript if the iRNA promotes cleavage of thetranscript anywhere within that particular site. Such an iRNA willgenerally include at least about 15 contiguous nucleotides from one ofthe sequences provided in Table 1 coupled to additional nucleotidesequences taken from the region contiguous to the selected sequence in aPCSK9 gene.

While a target sequence is generally about 15-30 nucleotides in length,there is wide variation in the suitability of particular sequences inthis range for directing cleavage of any given target RNA. Varioussoftware packages and the guidelines set out herein provide guidance forthe identification of optimal target sequences for any given genetarget, but an empirical approach can also be taken in which a “window”or “mask” of a given size (as a non-limiting example, 21 nucleotides) isliterally or figuratively (including, e.g., in silico) placed on thetarget RNA sequence to identify sequences in the size range that canserve as target sequences. By moving the sequence “window” progressivelyone nucleotide upstream or downstream of an initial target sequencelocation, the next potential target sequence can be identified, untilthe complete set of possible sequences is identified for any giventarget size selected. This process, coupled with systematic synthesisand testing of the identified sequences (using assays as describedherein or as known in the art) to identify those sequences that performoptimally can identify those RNA sequences that, when targeted with aniRNA agent, mediate the best inhibition of target gene expression. Thus,while the sequences identified, for example, in a Table 1 representeffective target sequences, it is contemplated that further optimizationof inhibition efficiency can be achieved by progressively “walking thewindow” one nucleotide upstream or downstream of the given sequences toidentify sequences with equal or better inhibition characteristics.

Further, it is contemplated that for any sequence identified, e.g., inTable 1, further optimization could be achieved by systematically eitheradding or removing nucleotides to generate longer or shorter sequencesand testing those sequences generated by walking a window of the longeror shorter size up or down the target RNA from that point. Again,coupling this approach to generating new candidate targets with testingfor effectiveness of iRNAs based on those target sequences in aninhibition assay as known in the art and/or as described herein can leadto further improvements in the efficiency of inhibition. Further still,such optimized sequences can be adjusted by, e.g., the introduction ofmodified nucleotides as described herein or as known in the art,addition or changes in overhang, or other modifications as known in theart and/or discussed herein to further optimize the molecule (e.g.,increasing serum stability or circulating half-life, increasing thermalstability, enhancing transmembrane delivery, targeting to a particularlocation or cell type, increasing interaction with silencing pathwayenzymes, increasing release from endosomes) as an expression inhibitor.

An iRNA as described herein can contain one or more mismatches to thetarget sequence. In one embodiment, an iRNA as described herein containsno more than 3 mismatches. If the antisense strand of the iRNA containsmismatches to a target sequence, it is preferable that the area ofmismatch is not located in the center of the region of complementarity.If the antisense strand of the iRNA contains mismatches to the targetsequence, it is preferable that the mismatch be restricted to be withinthe last 5 nucleotides from either the 5′- or 3′-end of the region ofcomplementarity. For example, for a 23 nucleotide iRNA agent the strandwhich is complementary to a region of a PCSK9 gene, generally does notcontain any mismatch within the central 13 nucleotides. The methodsdescribed herein or methods known in the art can be used to determinewhether an iRNA containing a mismatch to a target sequence is effectivein inhibiting the expression of a PCSK9 gene. Consideration of theefficacy of iRNAs with mismatches in inhibiting expression of a PCSK9gene is important, especially if the particular region ofcomplementarity in a PCSK9 gene is known to have polymorphic sequencevariation within the population.

The nucleic acids featured in the invention can be synthesized and/ormodified by methods well established in the art, such as those describedin “Current protocols in nucleic acid chemistry,” Beaucage, S. L. et al.(Edrs.), John Wiley & Sons, Inc., New York, N.Y., USA, which is herebyincorporated herein by reference. Modifications include, for example,end modifications, e.g., 5′-end modifications (phosphorylation,conjugation, inverted linkages) or 3′-end modifications (conjugation,DNA nucleotides, inverted linkages, etc.); base modifications, e.g.,replacement with stabilizing bases, destabilizing bases, or bases thatbase pair with an expanded repertoire of partners, removal of bases(abasic nucleotides), or conjugated bases; sugar modifications (e.g., atthe 2′-position or 4′-position) or replacement of the sugar; and/orbackbone modifications, including modification or replacement of thephosphodiester linkages. Specific examples of iRNA compounds useful inthe embodiments described herein include, but are not limited to RNAscontaining modified backbones or no natural internucleoside linkages.RNAs having modified backbones include, among others, those that do nothave a phosphorus atom in the backbone. For the purposes of thisspecification, and as sometimes referenced in the art, modified RNAsthat do not have a phosphorus atom in their internucleoside backbone canalso be considered to be oligonucleosides. In some embodiments, amodified iRNA will have a phosphorus atom in its internucleosidebackbone.

Modified RNA backbones include, for example, phosphorothioates, chiralphosphorothioates, phosphorodithioates, phosphotriesters,aminoalkylphosphotriesters, methyl and other alkyl phosphonatesincluding 3′-alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates including 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′-linked analogs ofthese, and those having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Varioussalts, mixed salts and free acid forms are also included.

Representative U.S. patents that teach the preparation of the abovephosphorus-containing linkages include, but are not limited to, U.S.Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,195;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253; 5,571,799;5,587,361; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170;6,172,209; 6,239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423;6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294;6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and U.S. Pat.RE39464, the entire contents of each of which are hereby incorporatedherein by reference.

Modified RNA backbones that do not include a phosphorus atom thereinhave backbones that are formed by short chain alkyl or cycloalkylinternucleoside linkages, mixed heteroatoms and alkyl or cycloalkylinternucleoside linkages, or one or more short chain heteroatomic orheterocyclic internucleoside linkages. These include those havingmorpholino linkages (formed in part from the sugar portion of anucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH₂ component parts.

Representative U.S. patents that teach the preparation of the aboveoligonucleosides include, but are not limited to, U.S. Pat. Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033;5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967;5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046;5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and,5,677,439, the entire contents of each of which are hereby incorporatedherein by reference.

In other embodiments, suitable RNA mimetics are contemplated for use iniRNAs, in which both the sugar and the internucleoside linkage, i.e.,the backbone, of the nucleotide units are replaced with novel groups.The base units are maintained for hybridization with an appropriatenucleic acid target compound. One such oligomeric compound, an RNAmimetic that has been shown to have excellent hybridization properties,is referred to as a peptide nucleic acid (PNA). In PNA compounds, thesugar backbone of an RNA is replaced with an amide containing backbone,in particular an aminoethylglycine backbone. The nucleobases areretained and are bound directly or indirectly to aza nitrogen atoms ofthe amide portion of the backbone. Representative U.S. patents thatteach the preparation of PNA compounds include, but are not limited to,U.S. Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, the entire contentsof each of which are hereby incorporated herein by reference. AdditionalPNA compounds suitable for use in the iRNAs of the invention aredescribed in, for example, in Nielsen et al., Science, 1991, 254,1497-1500.

Some embodiments featured in the invention include RNAs withphosphorothioate backbones and oligonucleosides with heteroatombackbones, and in particular —CH₂—NH—CH₂—, —CH₂—N(CH₃)—O—CH₂—[known as amethylene (methylimino) or MMI backbone], —CH₂—O—N(CH₃)—CH₂—,—CH₂—N(CH₃)—N(CH₃)—CH₂— and —N(CH₃)—CH₂—CH₂ [wherein the nativephosphodiester backbone is represented as —O—P—O—CH₂—] of theabove-referenced U.S. Pat. No. 5,489,677, and the amide backbones of theabove-referenced U.S. Pat. No. 5,602,240. In some embodiments, the RNAsfeatured herein have morpholino backbone structures of theabove-referenced U.S. Pat. No. 5,034,506.

Modified RNAs can also contain one or more substituted sugar moieties.The iRNAs, e.g., dsRNAs, featured herein can include one of thefollowing at the 2′-position: OH; F; O-, S-, or N-alkyl; O-, S-, orN-alkenyl; O-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl,alkenyl and alkynyl can be substituted or unsubstituted C₁ to C₁₀ alkylor C₂ to C₁₀ alkenyl and alkynyl. Exemplary suitable modificationsinclude O[(CH₂)_(n)O]_(m)CH₃, O(CH₂)._(n)OCH₃, O(CH₂)_(n)NH₂,O(CH₂)_(n)CH₃, O(CH₂)_(n)ONH₂, and O(CH₂)_(n)ON[(CH₂)_(n)CH₃)]₂, where nand m are from 1 to about 10. In other embodiments, dsRNAs include oneof the following at the 2′ position: C₁ to C₁₀ lower alkyl, substitutedlower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN,Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂,heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino,substituted silyl, an RNA cleaving group, a reporter group, anintercalator, a group for improving the pharmacokinetic properties of aniRNA, or a group for improving the pharmacodynamic properties of aniRNA, and other substituents having similar properties. In someembodiments, the modification includes a 2′-methoxyethoxy(2′-O—CH₂CH₂OCH₃, also known as 2′-O-(2-methoxyethyl) or 2′-MOE) (Martinet al., Helv. Chim. Acta, 1995, 78:486-504) i.e., an alkoxy-alkoxygroup. Another exemplary modification is 2′-dimethylaminooxyethoxy,i.e., a O(CH₂)₂ON(CH₃)₂ group, also known as 2′-DMAOE, as described inexamples herein below, and 2′-dimethylaminoethoxyethoxy (also known inthe art as 2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e.,2′-O—CH₂—O—CH₂—N(CH₂)₂.

Other modifications include 2′-methoxy (2′-OCH₃), 2′-aminopropoxy(2′-OCH₂CH₂CH₂NH₂) and 2′-fluoro (2′-F). Similar modifications can alsobe made at other positions on the RNA of an iRNA, particularly the 3′position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linkeddsRNAs and the 5′ position of 5′ terminal nucleotide. iRNAs can alsohave sugar mimetics such as cyclobutyl moieties in place of thepentofuranosyl sugar. Representative U.S. patents that teach thepreparation of such modified sugar structures include, but are notlimited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044;5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811;5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873;5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which arecommonly owned with the instant application. The entire contents of eachof the foregoing are hereby incorporated herein by reference.

The RNA of an iRNA can also include nucleobase (often referred to in theart simply as “base”) modifications or substitutions. As used herein,“unmodified” or “natural” nucleobases include the purine bases adenine(A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C)and uracil (U). Modified nucleobases include other synthetic and naturalnucleobases such as deoxy-thymine (dT), 5-methylcytosine (5-me-C),5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine,6-methyl and other alkyl derivatives of adenine and guanine, 2-propyland other alkyl derivatives of adenine and guanine, 2-thiouracil,2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyluracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil(pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl,8-hydroxyl anal other 8-substituted adenines and guanines, 5-halo,particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracilsand cytosines, 7-methylguanine and 7-methyladenine, 8-azaguanine and8-azaadenine, 7-deazaguanine and 7-daazaadenine and 3-deazaguanine and3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat.No. 3,687,808, those disclosed in Modified Nucleosides in Biochemistry,Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; thosedisclosed in The Concise Encyclopedia Of Polymer Science AndEngineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons,1990, these disclosed by Englisch et al., Angewandte Chemie,International Edition, 1991, 30, 613, and those disclosed by Sanghvi, YS., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke,S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobasesare particularly useful for increasing the binding affinity of theoligomeric compounds featured in the invention. These include5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6substituted purines, including 2-aminopropyladenine, 5-propynyluraciland 5-propynylcytosine. 5-methylcytosine substitutions have been shownto increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y.S., Crooke, S. T. and Lebleu, B., Eds., dsRNA Research and Applications,CRC Press, Boca Raton, 1993, pp. 276-278) and are exemplary basesubstitutions, even more particularly when combined with2′-O-methoxyethyl sugar modifications.

Representative U.S. patents that teach the preparation of certain of theabove noted modified nucleobases as well as other modified nucleobasesinclude, but are not limited to, the above noted U.S. Pat. Nos.3,687,808, 4,845,205; 5,130,30; 5,134,066; 5,175,273; 5,367,066;5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711;5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,681,941;5,750,692; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887;6,380,368; 6,528,640; 6,639,062; 6,617,438; 7,045,610; 7,427,672; and7,495,088, the entire contents of each of which are hereby incorporatedherein by reference.

The RNA of an iRNA can also be modified to include one or more bicyclicsugar moities. A “bicyclic sugar” is a furanosyl ring modified by thebridging of two atoms. A “bicyclic nucleoside” (“BNA”) is a nucleosidehaving a sugar moiety comprising a bridge connecting two carbon atoms ofthe sugar ring, thereby forming a bicyclic ring system. In certainembodiments, the bridge connects the 4′-carbon and the 2′-carbon of thesugar ring. Thus, in some embodiments an agent of the invention mayinclude the RNA of an iRNA can also be modified to include one or morelocked nucleic acids (LNA). A locked nucleic acid is a nucleotide havinga modified ribose moiety in which the ribose moiety comprises an extrabridge connecting the 2′ and 4′ carbons. In other words, an LNA is anucleotide comprising a bicyclic sugar moiety comprising a 4′-CH2-O-2′bridge. This structure effectively “locks” the ribose in the 3′-endostructural conformation. The addition of locked nucleic acids to siRNAshas been shown to increase siRNA stability in serum, and to reduceoff-target effects (Elmen, J. et al., (2005) Nucleic Acids Research33(1):439-447; Mook, O R. et al., (2007) Mol Canc Ther 6(3):833-843;Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193).

Examples of bicyclic nucleosides for use in the polynucleotides of theinvention include without limitation nucleosides comprising a bridgebetween the 4′ and the 2′ ribosyl ring atoms. In certain embodiments,the antisense polynucleotide agents of the invention include one or morebicyclic nucleosides comprising a 4′ to 2′ bridge. Examples of such 4′to 2′ bridged bicyclic nucleosides, include but are not limited to4′-(CH₂)—O-2′ (LNA); 4′-(CH₂)—S-2′; 4′-(CH₂)₂—O-2′ (ENA);4′-CH(CH₃)—O-2′ (also referred to as “constrained ethyl” or “cEt”) and4′-CH(CH₂OCH₃)—O-2′ (and analogs thereof; see, e.g., U.S. Pat. No.7,399,845); 4′-C(CH₃)(CH₃)—O-2′ (and analogs thereof; see e.g., U.S.Pat. No. 8,278,283); 4′-CH₂—N(OCH₃)-2′ (and analogs thereof; see e.g.,U.S. Pat. No. 8,278,425); 4′-CH2-O—N(CH3)-2′ (see, e.g., U.S. PatentPublication No. 2004/0171570); 4′-CH2-N(R)—O-2′, wherein R is H, C1-C12alkyl, or a protecting group (see, e.g., U.S. Pat. No. 7,427,672);4′-CH2-C(H)(CH3)-2′ (see, e.g., Chattopadhyaya et al., J. Org. Chem.,2009, 74, 118-134); and 4′-CH2-C(═CH2)-2′ (and analogs thereof; see,e.g., U.S. Pat. No. 8,278,426). The entire contents of each of theforegoing are hereby incorporated herein by reference.

Additional representative U.S. patents and US patent Publications thatteach the preparation of locked nucleic acid nucleotides include, butare not limited to, the following: U.S. Pat. Nos. 6,268,490; 6,525,191;6,670,461; 6,770,748; 6,794,499; 6,998,484; 7,053,207; 7,034,133;7,084,125; 7,399,845; 7,427,672; 7,569,686; 7,741,457; 8,022,193;8,030,467; 8,278,425; 8,278,426; 8,278,283; US 2008/0039618; and US2009/0012281, the entire contents of each of which are herebyincorporated herein by reference.

Any of the foregoing bicyclic nucleosides can be prepared having one ormore stereochemical sugar configurations including for exampleα-L-ribofuranose and β-D-ribofuranose (see WO 99/14226).

The RNA of an iRNA can also be modified to include one or moreconstrained ethyl nucleotides. As used herein, a “constrained ethylnucleotide” or “cEt” is a locked nucleic acid comprising a bicyclicsugar moiety comprising a 4′-CH(CH₃)—O-2′ bridge. In one embodiment, aconstrained ethyl nucleotide is in the S conformation referred to hereinas “S-cEt.”

An iRNA of the invention may also include one or more “conformationallyrestricted nucleotides” (“CRN”). CRN are nucleotide analogs with alinker connecting the C2′ and C4′ carbons of ribose or the C3 and -C5′carbons of ribose. CRN lock the ribose ring into a stable conformationand increase the hybridization affinity to mRNA. The linker is ofsufficient length to place the oxygen in an optimal position forstability and affinity resulting in less ribose ring puckering.

Representative publications that teach the preparation of certain of theabove noted CRN include, but are not limited to, US Patent PublicationNo. 2013/0190383; and PCT publication WO 2013/036868, the entirecontents of each of which are hereby incorporated herein by reference.

One or more of the nucleotides of an iRNA of the invention may alsoinclude a hydroxymethyl substituted nucleotide. A “hydroxymethylsubstituted nucleotide” is an acyclic 2′-3′-seco-nucleotide, alsoreferred to as an “unlocked nucleic acid” (“UNA”) modification

Representative U.S. publications that teach the preparation of UNAinclude, but are not limited to, U.S. Pat. No. 8,314,227; and US PatentPublication Nos. 2013/0096289; 2013/0011922; and 2011/0313020, theentire contents of each of which are hereby incorporated herein byreference.

Other modifications of the nucleotides of an iRNA of the inventioninclude a 5′ phosphate or 5′ phosphate mimic, e.g., a 5′-terminalphosphate or phosphate mimic on the antisense strand of an RNAi agent.Suitable phosphate mimics are disclosed in, for example US PatentPublication No. 2012/0157511, the entire contents of which areincorporated herein by reference.

Potentially stabilizing modifications to the ends of RNA molecules caninclude N-(acetylaminocaproyl)-4-hydroxyprolinol (Hyp-C6-NHAc),N-(caproyl-4-hydroxyprolinol (Hyp-C6), N-(acetyl-4-hydroxyprolinol(Hyp-NHAc), thymidine-2′-O-deoxythymidine (ether),N-(aminocaproyl)-4-hydroxyprolinol (Hyp-C6-amino),2-docosanoyl-uridine-3″-phosphate, inverted base dT(idT) and others.Disclosure of this modification can be found in PCT Publication No. WO2011/005861.

A. Modified iRNAs Comprising Motifs

In certain aspects of the invention, the double-stranded RNAi agents ofthe invention include agents with chemical modifications as disclosed,for example, in U.S. Patent Publication No. 2014/0315835 and PCTPublication No. WO 2013/075035, the entire contents of each of which areincorporated herein by reference, the entire contents of each of whichare incorporated herein by reference. As shown herein and in U.S. PatentPublication No. 2014/0315835 and PCT Publication No. WO 2013/075035, asuperior result may be obtained by introducing one or more motifs ofthree identical modifications on three consecutive nucleotides into asense strand and/or antisense strand of an RNAi agent, particularly ator near the cleavage site. In some embodiments, the sense strand andantisense strand of the RNAi agent may otherwise be completely modified.The introduction of these motifs interrupts the modification pattern, ifpresent, of the sense and/or antisense strand. The RNAi agent may beoptionally conjugated with a GalNAc derivative ligand, for instance onthe sense strand. The resulting RNAi agents present superior genesilencing activity.

More specifically, it has been surprisingly discovered that when thesense strand and antisense strand of the double-stranded RNAi agent arecompletely modified to have one or more motifs of three identicalmodifications on three consecutive nucleotides at or near the cleavagesite of at least one strand of an RNAi agent, the gene silencingactivity of the RNAi agent was superiorly enhanced.

Accordingly, the invention provides double-stranded RNAi agents capableof inhibiting the expression of a target gene (i.e., a PCSK9 gene) invivo. The RNAi agent comprises a sense strand and an antisense strand.Each strand of the RNAi agent may range from 12-30 nucleotides inlength. For example, each strand may be between 14-30 nucleotides inlength, 17-30 nucleotides in length, 25-30 nucleotides in length, 27-30nucleotides in length, 17-23 nucleotides in length, 17-21 nucleotides inlength, 17-19 nucleotides in length, 19-25 nucleotides in length, 19-23nucleotides in length, 19-21 nucleotides in length, 21-25 nucleotides inlength, or 21-23 nucleotides in length.

The sense strand and antisense strand typically form a duplex doublestranded RNA (“dsRNA”), also referred to herein as an “RNAi agent.” Theduplex region of an RNAi agent may be 12-30 nucleotide pairs in length.For example, the duplex region can be between 14-30 nucleotide pairs inlength, 17-30 nucleotide pairs in length, 27-30 nucleotide pairs inlength, 17-23 nucleotide pairs in length, 17-21 nucleotide pairs inlength, 17-19 nucleotide pairs in length, 19-25 nucleotide pairs inlength, 19-23 nucleotide pairs in length, 19-21 nucleotide pairs inlength, 21-25 nucleotide pairs in length, or 21-23 nucleotide pairs inlength. In another example, the duplex region is selected from 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, and 27 nucleotides in length.

In one embodiment, the RNAi agent may contain one or more overhangregions and/or capping groups at the 3′-end, 5′-end, or both ends of oneor both strands. The overhang can be 1-6 nucleotides in length, forinstance 2-6 nucleotides in length, 1-5 nucleotides in length, 2-5nucleotides in length, 1-4 nucleotides in length, 2-4 nucleotides inlength, 1-3 nucleotides in length, 2-3 nucleotides in length, or 1-2nucleotides in length. The overhangs can be the result of one strandbeing longer than the other, or the result of two strands of the samelength being staggered. The overhang can form a mismatch with the targetmRNA or it can be complementary to the gene sequences being targeted orcan be another sequence. The first and second strands can also bejoined, e.g., by additional bases to form a hairpin, or by othernon-base linkers.

In one embodiment, the nucleotides in the overhang region of the RNAiagent can each independently be a modified or unmodified nucleotideincluding, but no limited to 2′-sugar modified, such as, 2-F,2′-Omethyl, thymidine (T), 2′-O-methoxyethyl-5-methyluridine (Teo),2′-O-methoxyethyladenosine (Aeo), 2′-O-methoxyethyl-5-methylcytidine(m5Ceo), and any combinations thereof. For example, TT can be anoverhang sequence for either end on either strand. The overhang can forma mismatch with the target mRNA or it can be complementary to the genesequences being targeted or can be another sequence.

The 5′- or 3′-overhangs at the sense strand, antisense strand or bothstrands of the RNAi agent may be phosphorylated. In some embodiments,the overhang region(s) contains two nucleotides having aphosphorothioate between the two nucleotides, where the two nucleotidescan be the same or different. In one embodiment, the overhang is presentat the 3′-end of the sense strand, antisense strand, or both strands. Inone embodiment, this 3′-overhang is present in the antisense strand. Inone embodiment, this 3′-overhang is present in the sense strand.

The RNAi agent may contain only a single overhang, which can strengthenthe interference activity of the RNAi, without affecting its overallstability. For example, the single-stranded overhang may be located atthe 3′-terminal end of the sense strand or, alternatively, at the3′-terminal end of the antisense strand. The RNAi may also have a bluntend, located at the 5′-end of the antisense strand (or the 3′-end of thesense strand) or vice versa. Generally, the antisense strand of the RNAihas a nucleotide overhang at the 3′-end, and the 5′-end is blunt. Whilenot wishing to be bound by theory, the asymmetric blunt end at the5′-end of the antisense strand and 3′-end overhang of the antisensestrand favor the guide strand loading into RISC process.

In one embodiment, the RNAi agent is a double ended bluntmer of 19nucleotides in length, wherein the sense strand contains at least onemotif of three 2′-F modifications on three consecutive nucleotides atpositions 7, 8, 9 from the 5′end. The antisense strand contains at leastone motif of three 2′-O-methyl modifications on three consecutivenucleotides at positions 11, 12, 13 from the 5′end.

In another embodiment, the RNAi agent is a double ended bluntmer of 20nucleotides in length, wherein the sense strand contains at least onemotif of three 2′-F modifications on three consecutive nucleotides atpositions 8, 9, 10 from the 5′end. The antisense strand contains atleast one motif of three 2′-O-methyl modifications on three consecutivenucleotides at positions 11, 12, 13 from the 5′end.

In yet another embodiment, the RNAi agent is a double ended bluntmer of21 nucleotides in length, wherein the sense strand contains at least onemotif of three 2′-F modifications on three consecutive nucleotides atpositions 9, 10, 11 from the 5′end. The antisense strand contains atleast one motif of three 2′-O-methyl modifications on three consecutivenucleotides at positions 11, 12, 13 from the 5′end.

In one embodiment, the RNAi agent comprises a 21 nucleotide sense strandand a 23 nucleotide antisense strand, wherein the sense strand containsat least one motif of three 2′-F modifications on three consecutivenucleotides at positions 9, 10, 11 from the 5′end; the antisense strandcontains at least one motif of three 2′-O-methyl modifications on threeconsecutive nucleotides at positions 11, 12, 13 from the 5′end, whereinone end of the RNAi agent is blunt, while the other end comprises a 2nucleotide overhang. Preferably, the 2 nucleotide overhang is at the3′-end of the antisense strand. When the 2 nucleotide overhang is at the3′-end of the antisense strand, there may be two phosphorothioateinternucleotide linkages between the terminal three nucleotides, whereintwo of the three nucleotides are the overhang nucleotides, and the thirdnucleotide is a paired nucleotide next to the overhang nucleotide. Inone embodiment, the RNAi agent additionally has two phosphorothioateinternucleotide linkages between the terminal three nucleotides at boththe 5′-end of the sense strand and at the 5′-end of the antisensestrand. In one embodiment, every nucleotide in the sense strand and theantisense strand of the RNAi agent, including the nucleotides that arepart of the motifs are modified nucleotides. In one embodiment eachresidue is independently modified with a 2′-O-methyl or 3′-fluoro, e.g.,in an alternating motif. Optionally, the RNAi agent further comprises aligand (preferably GalNAc₃).

In one embodiment, the RNAi agent comprises a sense and an antisensestrand, wherein the sense strand is 25-30 nucleotide residues in length,wherein starting from the 5′ terminal nucleotide (position 1) positions1 to 23 of the first strand comprise at least 8 ribonucleotides; theantisense strand is 36-66 nucleotide residues in length and, startingfrom the 3′ terminal nucleotide, comprises at least 8 ribonucleotides inthe positions paired with positions 1-23 of sense strand to form aduplex; wherein at least the 3 ‘ terminal nucleotide of antisense strandis unpaired with sense strand, and up to 6 consecutive 3’ terminalnucleotides are unpaired with sense strand, thereby forming a 3′ singlestranded overhang of 1-6 nucleotides; wherein the 5′ terminus ofantisense strand comprises from 10-30 consecutive nucleotides which areunpaired with sense strand, thereby forming a 10-30 nucleotide singlestranded 5′ overhang; wherein at least the sense strand 5′ terminal and3′ terminal nucleotides are base paired with nucleotides of antisensestrand when sense and antisense strands are aligned for maximumcomplementarity, thereby forming a substantially duplexed region betweensense and antisense strands; and antisense strand is sufficientlycomplementary to a target RNA along at least 19 ribonucleotides ofantisense strand length to reduce target gene expression when the doublestranded nucleic acid is introduced into a mammalian cell; and whereinthe sense strand contains at least one motif of three 2′-F modificationson three consecutive nucleotides, where at least one of the motifsoccurs at or near the cleavage site. The antisense strand contains atleast one motif of three 2′-O-methyl modifications on three consecutivenucleotides at or near the cleavage site.

In one embodiment, the RNAi agent comprises sense and antisense strands,wherein the RNAi agent comprises a first strand having a length which isat least 25 and at most 29 nucleotides and a second strand having alength which is at most 30 nucleotides with at least one motif of three2′-O-methyl modifications on three consecutive nucleotides at position11, 12, 13 from the 5′ end; wherein the 3′ end of the first strand andthe 5′ end of the second strand form a blunt end and the second strandis 1˜4 nucleotides longer at its 3′ end than the first strand, whereinthe duplex region which is at least 25 nucleotides in length, and thesecond strand is sufficiently complementary to a target mRNA along atleast 19 nucleotide of the second strand length to reduce target geneexpression when the RNAi agent is introduced into a mammalian cell, andwherein dicer cleavage of the RNAi agent preferentially results in ansiRNA comprising the 3′ end of the second strand, thereby reducingexpression of the target gene in the mammal. Optionally, the RNAi agentfurther comprises a ligand.

In one embodiment, the sense strand of the RNAi agent contains at leastone motif of three identical modifications on three consecutivenucleotides, where one of the motifs occurs at the cleavage site in thesense strand.

In one embodiment, the antisense strand of the RNAi agent can alsocontain at least one motif of three identical modifications on threeconsecutive nucleotides, where one of the motifs occurs at or near thecleavage site in the antisense strand

For an RNAi agent having a duplex region of 17-23 nucleotide in length,the cleavage site of the antisense strand is typically around the 10, 11and 12 positions from the 5′-end. Thus the motifs of three identicalmodifications may occur at the 9, 10, 11 positions; 10, 11, 12positions; 11, 12, 13 positions; 12, 13, 14 positions; or 13, 14, 15positions of the antisense strand, the count starting from the 1^(st)nucleotide from the 5′-end of the antisense strand, or, the countstarting from the 1^(st) paired nucleotide within the duplex region fromthe 5′-end of the antisense strand. The cleavage site in the antisensestrand may also change according to the length of the duplex region ofthe RNAi from the 5′-end.

The sense strand of the RNAi agent may contain at least one motif ofthree identical modifications on three consecutive nucleotides at thecleavage site of the strand; and the antisense strand may have at leastone motif of three identical modifications on three consecutivenucleotides at or near the cleavage site of the strand. When the sensestrand and the antisense strand form a dsRNA duplex, the sense strandand the antisense strand can be so aligned that one motif of the threenucleotides on the sense strand and one motif of the three nucleotideson the antisense strand have at least one nucleotide overlap, i.e., atleast one of the three nucleotides of the motif in the sense strandforms a base pair with at least one of the three nucleotides of themotif in the antisense strand. Alternatively, at least two nucleotidesmay overlap, or all three nucleotides may overlap.

In one embodiment, the sense strand of the RNAi agent may contain morethan one motif of three identical modifications on three consecutivenucleotides. The first motif may occur at or near the cleavage site ofthe strand and the other motifs may be a wing modification. The term“wing modification” herein refers to a motif occurring at anotherportion of the strand that is separated from the motif at or near thecleavage site of the same strand. The wing modification is eitheradjacent to the first motif or is separated by at least one or morenucleotides. When the motifs are immediately adjacent to each other thenthe chemistry of the motifs are distinct from each other and when themotifs are separated by one or more nucleotide than the chemistries canbe the same or different. Two or more wing modifications may be present.For instance, when two wing modifications are present, each wingmodification may occur at one end relative to the first motif which isat or near cleavage site or on either side of the lead motif.

Like the sense strand, the antisense strand of the RNAi agent maycontain more than one motifs of three identical modifications on threeconsecutive nucleotides, with at least one of the motifs occurring at ornear the cleavage site of the strand. This antisense strand may alsocontain one or more wing modifications in an alignment similar to thewing modifications that may be present on the sense strand.

In one embodiment, the wing modification on the sense strand orantisense strand of the RNAi agent typically does not include the firstone or two terminal nucleotides at the 3′-end, 5′-end or both ends ofthe strand.

In another embodiment, the wing modification on the sense strand orantisense strand of the RNAi agent typically does not include the firstone or two paired nucleotides within the duplex region at the 3′-end,5′-end or both ends of the strand.

When the sense strand and the antisense strand of the RNAi agent eachcontain at least one wing modification, the wing modifications may fallon the same end of the duplex region, and have an overlap of one, two orthree nucleotides.

When the sense strand and the antisense strand of the RNAi agent eachcontain at least two wing modifications, the sense strand and theantisense strand can be so aligned that two modifications each from onestrand fall on one end of the duplex region, having an overlap of one,two or three nucleotides; two modifications each from one strand fall onthe other end of the duplex region, having an overlap of one, two orthree nucleotides; two modifications one strand fall on each side of thelead motif, having an overlap of one, two or three nucleotides in theduplex region.

In one embodiment, every nucleotide in the sense strand and antisensestrand of the RNAi agent, including the nucleotides that are part of themotifs, may be modified. Each nucleotide may be modified with the sameor different modification which can include one or more alteration ofone or both of the non-linking phosphate oxygens and/or of one or moreof the linking phosphate oxygens; alteration of a constituent of theribose sugar, e.g., of the 2′ hydroxyl on the ribose sugar; wholesalereplacement of the phosphate moiety with “dephospho” linkers;modification or replacement of a naturally occurring base; andreplacement or modification of the ribose-phosphate backbone.

As nucleic acids are polymers of subunits, many of the modificationsoccur at a position which is repeated within a nucleic acid, e.g., amodification of a base, or a phosphate moiety, or a non-linking O of aphosphate moiety. In some cases the modification will occur at all ofthe subject positions in the nucleic acid but in many cases it will not.By way of example, a modification may only occur at a 3′ or 5′ terminalposition, may only occur in a terminal region, e.g., at a position on aterminal nucleotide or in the last 2, 3, 4, 5, or 10 nucleotides of astrand. A modification may occur in a double strand region, a singlestrand region, or in both. A modification may occur only in the doublestrand region of a RNA or may only occur in a single strand region of aRNA. For example, a phosphorothioate modification at a non-linking Oposition may only occur at one or both termini, may only occur in aterminal region, e.g., at a position on a terminal nucleotide or in thelast 2, 3, 4, 5, or 10 nucleotides of a strand, or may occur in doublestrand and single strand regions, particularly at termini. The 5′ end orends can be phosphorylated.

It may be possible, e.g., to enhance stability, to include particularbases in overhangs, or to include modified nucleotides or nucleotidesurrogates, in single strand overhangs, e.g., in a 5′ or 3′ overhang, orin both. For example, it can be desirable to include purine nucleotidesin overhangs. In some embodiments all or some of the bases in a 3′ or 5′overhang may be modified, e.g., with a modification described herein.Modifications can include, e.g., the use of modifications at the 2′position of the ribose sugar with modifications that are known in theart, e.g., the use of deoxyribonucleotides, 2′-deoxy-2′-fluoro (2′-F) or2′-O-methyl modified instead of the ribosugar of the nucleobase, andmodifications in the phosphate group, e.g., phosphorothioatemodifications. Overhangs need not be homologous with the targetsequence. In one embodiment, each residue of the sense strand andantisense strand is independently modified with LNA, HNA, CeNA,2′-methoxyethyl, 2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-deoxy,2′-hydroxyl, or 2′-fluoro. The strands can contain more than onemodification. In one embodiment, each residue of the sense strand andantisense strand is independently modified with 2′-O-methyl or2′-fluoro.

At least two different modifications are typically present on the sensestrand and antisense strand. Those two modifications may be the2′-O-methyl or 2′-fluoro modifications, or others.

In one embodiment, the N_(a) and/or N_(b) comprise modifications of analternating pattern. The term “alternating motif” as used herein refersto a motif having one or more modifications, each modification occurringon alternating nucleotides of one strand. The alternating nucleotide mayrefer to one per every other nucleotide or one per every threenucleotides, or a similar pattern. For example, if A, B and C eachrepresent one type of modification to the nucleotide, the alternatingmotif can be “ABABABABABAB . . . ,” “AABBAABBAABB . . . ,” “AABAABAABAAB. . . ,” “AAABAAABAAAB . . . ,” “AAABBBAAABBB . . . ,” or “ABCABCABCABC. . . ,” etc.

The type of modifications contained in the alternating motif may be thesame or different. For example, if A, B, C, D each represent one type ofmodification on the nucleotide, the alternating pattern, i.e.,modifications on every other nucleotide, may be the same, but each ofthe sense strand or antisense strand can be selected from severalpossibilities of modifications within the alternating motif such as“ABABAB . . . ”, “ACACAC . . . ” “BDBDBD . . . ” or “CDCDCD . . . ,”etc.

In one embodiment, the RNAi agent of the invention comprises themodification pattern for the alternating motif on the sense strandrelative to the modification pattern for the alternating motif on theantisense strand is shifted. The shift may be such that the modifiedgroup of nucleotides of the sense strand corresponds to a differentlymodified group of nucleotides of the antisense strand and vice versa.For example, the sense strand when paired with the antisense strand inthe dsRNA duplex, the alternating motif in the sense strand may startwith “ABABAB” from 5′-3′ of the strand and the alternating motif in theantisense strand may start with “BABABA” from 5′-3′ of the strand withinthe duplex region. As another example, the alternating motif in thesense strand may start with “AABBAABB” from 5′-3′ of the strand and thealternating motif in the antisense strand may start with “BBAABBAA” from5′-3′ of the strand within the duplex region, so that there is acomplete or partial shift of the modification patterns between the sensestrand and the antisense strand.

In one embodiment, the RNAi agent comprises the pattern of thealternating motif of 2′-O-methyl modification and 2′-F modification onthe sense strand initially has a shift relative to the pattern of thealternating motif of 2′-O-methyl modification and 2′-F modification onthe antisense strand initially, i.e., the 2′-O-methyl modifiednucleotide on the sense strand base pairs with a 2′-F modifiednucleotide on the antisense strand and vice versa. The 1 position of thesense strand may start with the 2′-F modification, and the 1 position ofthe antisense strand may start with the 2′-O-methyl modification.

The introduction of one or more motifs of three identical modificationson three consecutive nucleotides to the sense strand and/or antisensestrand interrupts the initial modification pattern present in the sensestrand and/or antisense strand. This interruption of the modificationpattern of the sense and/or antisense strand by introducing one or moremotifs of three identical modifications on three consecutive nucleotidesto the sense and/or antisense strand surprisingly enhances the genesilencing activity to the target gene.

In one embodiment, when the motif of three identical modifications onthree consecutive nucleotides is introduced to any of the strands, themodification of the nucleotide next to the motif is a differentmodification than the modification of the motif. For example, theportion of the sequence containing the motif is “ . . . N_(a)YYYN_(b) .. . ,” where “Y” represents the modification of the motif of threeidentical modifications on three consecutive nucleotide, and “N_(a)” and“N_(b)” represent a modification to the nucleotide next to the motif“YYY” that is different than the modification of Y, and where N_(a) andN_(b) can be the same or different modifications. Alternatively, N_(a)and/or N_(b) may be present or absent when there is a wing modificationpresent.

The RNAi agent may further comprise at least one phosphorothioate ormethylphosphonate internucleotide linkage. The phosphorothioate ormethylphosphonate internucleotide linkage modification may occur on anynucleotide of the sense strand or antisense strand or both strands inany position of the strand. For instance, the internucleotide linkagemodification may occur on every nucleotide on the sense strand and/orantisense strand; each internucleotide linkage modification may occur inan alternating pattern on the sense strand and/or antisense strand; orthe sense strand or antisense strand may contain both internucleotidelinkage modifications in an alternating pattern. The alternating patternof the internucleotide linkage modification on the sense strand may bethe same or different from the antisense strand, and the alternatingpattern of the internucleotide linkage modification on the sense strandmay have a shift relative to the alternating pattern of theinternucleotide linkage modification on the antisense strand. In oneembodiment, a double-stranded RNAi agent comprises 6-8 phosphorothioateinternucleotide linkages. In one embodiment, the antisense strandcomprises two phosphorothioate internucleotide linkages at the5′-terminus and two phosphorothioate internucleotide linkages at the3′-terminus, and the sense strand comprises at least twophosphorothioate internucleotide linkages at either the 5′-terminus orthe 3′-terminus.

In one embodiment, the RNAi comprises a phosphorothioate ormethylphosphonate internucleotide linkage modification in the overhangregion. For example, the overhang region may contain two nucleotideshaving a phosphorothioate or methylphosphonate internucleotide linkagebetween the two nucleotides. Internucleotide linkage modifications alsomay be made to link the overhang nucleotides with the terminal pairednucleotides within the duplex region. For example, at least 2, 3, 4, orall the overhang nucleotides may be linked through phosphorothioate ormethylphosphonate internucleotide linkage, and optionally, there may beadditional phosphorothioate or methylphosphonate internucleotidelinkages linking the overhang nucleotide with a paired nucleotide thatis next to the overhang nucleotide. For instance, there may be at leasttwo phosphorothioate internucleotide linkages between the terminal threenucleotides, in which two of the three nucleotides are overhangnucleotides, and the third is a paired nucleotide next to the overhangnucleotide. These terminal three nucleotides may be at the 3′-end of theantisense strand, the 3′-end of the sense strand, the 5′-end of theantisense strand, and/or the 5′end of the antisense strand.

In one embodiment, the 2 nucleotide overhang is at the 3′-end of theantisense strand, and there are two phosphorothioate internucleotidelinkages between the terminal three nucleotides, wherein two of thethree nucleotides are the overhang nucleotides, and the third nucleotideis a paired nucleotide next to the overhang nucleotide. Optionally, theRNAi agent may additionally have two phosphorothioate internucleotidelinkages between the terminal three nucleotides at both the 5′-end ofthe sense strand and at the 5′-end of the antisense strand.

In one embodiment, the RNAi agent comprises mismatch(es) with thetarget, within the duplex, or combinations thereof. The mismatch mayoccur in the overhang region or the duplex region. The base pair may beranked on the basis of their propensity to promote dissociation ormelting (e.g., on the free energy of association or dissociation of aparticular pairing, the simplest approach is to examine the pairs on anindividual pair basis, though next neighbor or similar analysis can alsobe used). In terms of promoting dissociation: A:U is preferred over G:C;G:U is preferred over G:C; and I:C is preferred over G:C (I=inosine).Mismatches, e.g., non-canonical or other than canonical pairings (asdescribed elsewhere herein) are preferred over canonical (A:T, A:U, G:C)pairings; and pairings which include a universal base are preferred overcanonical pairings.

In one embodiment, the RNAi agent comprises at least one of the first 1,2, 3, 4, or 5 base pairs within the duplex regions from the 5′-end ofthe antisense strand independently selected from the group of: A:U, G:U,I:C, and mismatched pairs, e.g., non-canonical or other than canonicalpairings or pairings which include a universal base, to promote thedissociation of the antisense strand at the 5′-end of the duplex.

In one embodiment, the nucleotide at the 1 position within the duplexregion from the 5′-end in the antisense strand is selected from thegroup consisting of A, dA, dU, U, and dT. Alternatively, at least one ofthe first 1, 2 or 3 base pair within the duplex region from the 5′-endof the antisense strand is an AU base pair. For example, the first basepair within the duplex region from the 5′-end of the antisense strand isan AU base pair.

In another embodiment, the nucleotide at the 3′-end of the sense strandis deoxy-thymine (dT). In another embodiment, the nucleotide at the3′-end of the antisense strand is deoxy-thymine (dT). In one embodiment,there is a short sequence of deoxy-thymine nucleotides, for example, twodT nucleotides on the 3′-end of the sense and/or antisense strand.

In one embodiment, the sense strand sequence may be represented byformula (I):

5′n _(p)-N_(a)-(XXX)_(i)-N_(b)-YYY-N_(b)-(ZZZ)_(j)-N_(a)-n _(q)3′  (I)

wherein:

i and j are each independently 0 or 1;

p and q are each independently 0-6;

each N_(a) independently represents an oligonucleotide sequencecomprising 0-25 modified nucleotides, each sequence comprising at leasttwo differently modified nucleotides;each N_(b) independently represents an oligonucleotide sequencecomprising 0-10 modified nucleotides;each n_(p) and n_(q) independently represent an overhang nucleotide;wherein N_(b) and Y do not have the same modification; andXXX, YYY and ZZZ each independently represent one motif of threeidentical modifications on three consecutive nucleotides. Preferably YYYis all 2′-F modified nucleotides.In one embodiment, the N_(a) and/or N_(b) comprise modifications ofalternating pattern.

In one embodiment, the YYY motif occurs at or near the cleavage site ofthe sense strand. For example, when the RNAi agent has a duplex regionof 17-23 nucleotides in length, the YYY motif can occur at or thevicinity of the cleavage site (e.g.: can occur at positions 6, 7, 8, 7,8, 9, 8, 9, 10, 9, 10, 11, 10, 11, 12 or 11, 12, 13) of—the sensestrand, the count starting from the 1^(st) nucleotide, from the 5′-end;or optionally, the count starting at the 1^(st) paired nucleotide withinthe duplex region, from the 5′-end.

In one embodiment, i is 1 and j is 0, or i is 0 and j is 1, or both iand j are 1. The sense strand can therefore be represented by thefollowing formulas:

5′n _(p)-N_(a)-YYY-N_(b)-ZZZ-N_(a)-n _(q)3′  (Ib);

5′n _(p)-N_(a)-XXX-N_(b)-YYY-N_(a)-n _(q)3′  (Ic); or

5′n _(p)-N_(a)-XXX-N_(b)-YYY-N_(b)-ZZZ-N_(a)-n _(q)3′  (Id).

When the sense strand is represented by formula (Ib), N_(b) representsan oligonucleotide sequence comprising 0-10, 0-7, 0-5, 0-4, 0-2 or 0modified nucleotides. Each N_(a) independently can represent anoligonucleotide sequence comprising 2-20, 2-15, or 2-10 modifiednucleotides.

When the sense strand is represented as formula (Ic), N_(b) representsan oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7, 0-5, 0-4,0-2 or 0 modified nucleotides. Each N_(a) can independently represent anoligonucleotide sequence comprising 2-20, 2-15, or 2-10 modifiednucleotides.

When the sense strand is represented as formula (Id), each N_(b)independently represents an oligonucleotide sequence comprising 0-10,0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Preferably, N_(b) is 0, 1,2, 3, 4, 5 or 6 Each N_(a) can independently represent anoligonucleotide sequence comprising 2-20, 2-15, or 2-10 modifiednucleotides.

Each of X, Y and Z may be the same or different from each other.In other embodiments, i is 0 and j is 0, and the sense strand may berepresented by the formula:

5′n _(p)-N_(a)-YYY-N_(a)-n _(q)3′  (Ia).

When the sense strand is represented by formula (Ia), each N_(a)independently can represent an oligonucleotide sequence comprising 2-20,2-15, or 2-10 modified nucleotides.

In one embodiment, the antisense strand sequence of the RNAi may berepresented by formula (II):

5′n _(q′)-N_(a)′-(Z′Z′Z′)_(k)-N_(b)′-Y′Y′Y′-N_(b)′-(X′X′X′)_(l)-N′a-n_(p)′3′  (II)

wherein:

k and l are each independently 0 or 1;

p′ and q′ are each independently 0-6;

each N_(a)′ independently represents an oligonucleotide sequencecomprising 0-25 modified nucleotides, each sequence comprising at leasttwo differently modified nucleotides;each N_(b)′ independently represents an oligonucleotide sequencecomprising 0-10 modified nucleotides;each n_(p)′ and n_(q)′ independently represent an overhang nucleotide;wherein N_(b)′ and Y′ do not have the same modification;and X′X′X′, Y′Y′Y′ and Z′Z′Z′ each independently represent one motif ofthree identical modifications on three consecutive nucleotides.

In one embodiment, the N_(a)′ and/or N_(b)′ comprise modifications ofalternating pattern.

The Y′Y′Y′ motif occurs at or near the cleavage site of the antisensestrand. For example, when the RNAi agent has a duplex region of 17-23nucleotide in length, the Y′Y′Y′ motif can occur at positions 9, 10, 11;10, 11, 12; 11, 12, 13; 12, 13, 14; or 13, 14, 15 of the antisensestrand, with the count starting from the 1^(st) nucleotide, from the5′-end; or optionally, the count starting at the 1^(st) pairednucleotide within the duplex region, from the 5′-end. Preferably, theY′Y′Y′ motif occurs at positions 11, 12, 13.

In one embodiment, Y′Y′Y′ motif is all 2′-OMe modified nucleotides.

In one embodiment, k is 1 and 1 is 0, or k is 0 and 1 is 1, or both kand 1 are 1.

The antisense strand can therefore be represented by the followingformulas:

5′n _(q)′-N_(a)′-Z′Z′Z′-N_(b)′-Y′Y′Y′-N_(a)′-n _(p)′3′  (IIb);

5′n _(q)′-N_(a)′-Y′Y′Y′-N_(b)′-X′X′X′-n _(p)′3′  (IIc); or

5′n _(q)′-N_(a)′-Z′Z′Z′-N_(b)′-Y′Y′Y′-N_(b)′-X′X′X′-N_(a)′-n_(p)′3′  (IId).

When the antisense strand is represented by formula (IIb), N_(b)′represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7,0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a)′ independentlyrepresents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10modified nucleotides.

When the antisense strand is represented as formula (IIc), N_(b)′represents an oligonucleotide sequence comprising 0-10, 0-7, 0-10, 0-7,0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a)′ independentlyrepresents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10modified nucleotides.

When the antisense strand is represented as formula (IId), each N_(b)′independently represents an oligonucleotide sequence comprising 0-10,0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a)′independently represents an oligonucleotide sequence comprising 2-20,2-15, or 2-10 modified nucleotides. Preferably, N_(b) is 0, 1, 2, 3, 4,5 or 6. In other embodiments, k is 0 and 1 is 0 and the antisense strandmay be represented by the formula:

5′n _(p)′-N_(a)′-Y′Y′Y′-N_(a)-n _(q′)3′  (Ia).

When the antisense strand is represented as formula (IIa), each N_(a)′independently represents an oligonucleotide sequence comprising 2-20,2-15, or 2-10 modified nucleotides.

Each of X′, Y′ and Z′ may be the same or different from each other.Each nucleotide of the sense strand and antisense strand may beindependently modified with LNA, HNA, CeNA, 2′-methoxyethyl,2′-O-methyl, 2′-O-allyl, 2′-C-allyl, 2′-hydroxyl, or 2′-fluoro. Forexample, each nucleotide of the sense strand and antisense strand isindependently modified with 2′-O-methyl or 2′-fluoro. Each X, Y, Z, X′,Y′ and Z′, in particular, may represent a 2′-O-methyl modification or a2′-fluoro modification.

In one embodiment, the sense strand of the RNAi agent may contain YYYmotif occurring at 9, 10 and 11 positions of the strand when the duplexregion is 21 nt, the count starting from the 1^(st) nucleotide from the5′-end, or optionally, the count starting at the 1^(st) pairednucleotide within the duplex region, from the 5′-end; and Y represents2′-F modification. The sense strand may additionally contain XXX motifor ZZZ motifs as wing modifications at the opposite end of the duplexregion; and XXX and ZZZ each independently represents a 2′-OMemodification or 2′-F modification.

In one embodiment the antisense strand may contain Y′Y′Y′ motifoccurring at positions 11, 12, 13 of the strand, the count starting fromthe 1^(st) nucleotide from the 5′-end, or optionally, the count startingat the 1^(st) paired nucleotide within the duplex region, from the5′-end; and Y′ represents 2′-O-methyl modification. The antisense strandmay additionally contain X′X′X′ motif or Z′Z′Z′ motifs as wingmodifications at the opposite end of the duplex region; and X′X′X′ andZ′Z′Z′ each independently represents a 2′-OMe modification or 2′-Fmodification. The sense strand represented by any one of the aboveformulas (Ia), (Ib), (Ic), and (Id) forms a duplex with a antisensestrand being represented by any one of formulas (IIa), (IIb), (IIc), and(IId), respectively.

Accordingly, the RNAi agents for use in the methods of the invention maycomprise a sense strand and an antisense strand, each strand having 14to 30 nucleotides, the RNAi duplex represented by formula (III):

sense: 5′n _(p)-N_(a)-(XXX)_(i)-N_(b)-YYY-N_(b)-(ZZZ)_(j)—N_(a)-n _(q)3′

antisense: 3′n_(p)′-N_(a)′-(X′X′X′)_(k)-N_(b)′-Y′Y′Y′-N_(b)′-(Z′Z′Z′)_(l)-N_(a)′-n_(q)′5′   (III)

wherein:

-   -   j, k, and 1 are each independently 0 or 1;    -   p, p′, q, and q′ are each independently 0-6;        each N_(a) and N_(a)′ independently represents an        oligonucleotide sequence comprising 0-25 modified nucleotides,        each sequence comprising at least two differently modified        nucleotides;        each N_(b) and N_(b)′ independently represents an        oligonucleotide sequence comprising 0-10 modified nucleotides;        wherein        each n_(p)′, n_(p), n_(q)′, and n_(q), each of which may or may        not be present, independently represents an overhang nucleotide;        and        XXX, YYY, ZZZ, X′X′X′, Y′Y′Y′, and Z′Z′Z′ each independently        represent one motif of three identical modifications on three        consecutive nucleotides.

In one embodiment, i is 0 and j is 0; or i is 1 and j is 0; or i is 0and j is 1; or both i and j are 0; or both i and j are 1. In anotherembodiment, k is 0 and 1 is 0; or k is 1 and 1 is 0; k is 0 and 1 is 1;or both k and 1 are 0; or both k and 1 are 1.

Exemplary combinations of the sense strand and antisense strand forminga RNAi duplex include the formulas below:

5′n _(p)-N_(a)-YYY-N_(a)-n _(q)3′

3′n _(p)′-N_(a)′-Y′Y′Y′-N_(a) ′n _(q)′5′   (IIIa)

5′n _(p)-N_(a)-YYY-N_(b)-ZZZ-N_(a)-n _(q)3′

3′n _(p)′-N_(a)′-Y′Y′Y′-N_(b)′-Z′Z′Z′-N_(a) ′n _(q)′5′   (IIIb)

5′n _(p)-N_(a)-XXX-N_(b)-YYY-N_(a)-n _(q)3′

3′n _(p)′-N_(a)′-X′X′X′-N_(b)′-Y′Y′Y′-N_(a)′-n _(q)′5′   (IIIc)

5′n _(p)-N_(a)-XXX-N_(b)-YYY-N_(b)-ZZZ-N_(a)-n _(q)3′

3′n _(p)′-N_(a)′-X′X′X′-N_(b)′-Y′Y′Y′-N_(b)′-Z′Z′Z′-N_(a)-n _(q)′5′  (IIId)

When the RNAi agent is represented by formula (IIIa), each N_(a)independently represents an oligonucleotide sequence comprising 2-20,2-15, or 2-10 modified nucleotides.

When the RNAi agent is represented by formula (IIIb), each N_(b)independently represents an oligonucleotide sequence comprising 1-10,1-7, 1-5 or 1-4 modified nucleotides. Each N_(a) independentlyrepresents an oligonucleotide sequence comprising 2-20, 2-15, or 2-10modified nucleotides.

When the RNAi agent is represented as formula (IIIc), each N_(b), N_(b)′independently represents an oligonucleotide sequence comprising 0-10,0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a)independently represents an oligonucleotide sequence comprising 2-20,2-15, or 2-10 modified nucleotides.

When the RNAi agent is represented as formula (IIId), each N_(b), N_(b)′independently represents an oligonucleotide sequence comprising 0-10,0-7, 0-10, 0-7, 0-5, 0-4, 0-2 or 0 modified nucleotides. Each N_(a),N_(a)′ independently represents an oligonucleotide sequence comprising2-20, 2-15, or 2-10 modified nucleotides. Each of N_(a), N_(a)′, N_(b)and N_(b)′ independently comprises modifications of alternating pattern.

Each of X, Y and Z in formulas (III), (IIIa), (IIIb), (IIIc), and (IIId)may be the same or different from each other.

When the RNAi agent is represented by formula (III), (IIIa), (IIIb),(IIIc), and (IIId), at least one of the Y nucleotides may form a basepair with one of the Y′ nucleotides. Alternatively, at least two of theY nucleotides form base pairs with the corresponding Y′ nucleotides; orall three of the Y nucleotides all form base pairs with thecorresponding Y′ nucleotides.

When the RNAi agent is represented by formula (IIIb) or (IIId), at leastone of the Z nucleotides may form a base pair with one of the Z′nucleotides. Alternatively, at least two of the Z nucleotides form basepairs with the corresponding Z′ nucleotides; or all three of the Znucleotides all form base pairs with the corresponding Z′ nucleotides.

When the RNAi agent is represented as formula (IIIc) or (IIId), at leastone of the X nucleotides may form a base pair with one of the X′nucleotides. Alternatively, at least two of the X nucleotides form basepairs with the corresponding X′ nucleotides; or all three of the Xnucleotides all form base pairs with the corresponding X′ nucleotides.

In one embodiment, the modification on the Y nucleotide is differentthan the modification on the Y′ nucleotide, the modification on the Znucleotide is different than the modification on the Z′ nucleotide,and/or the modification on the X nucleotide is different than themodification on the X′ nucleotide.

In one embodiment, when the RNAi agent is represented by formula (IIId),the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications. Inanother embodiment, when the RNAi agent is represented by formula(IIId), the N_(a) modifications are 2′-O-methyl or 2′-fluoromodifications and n_(p)′>0 and at least one n_(p)′ is linked to aneighboring nucleotide a via phosphorothioate linkage. In yet anotherembodiment, when the RNAi agent is represented by formula (IIId), theN_(a) modifications are 2′-O-methyl or 2′-fluoro modifications, n_(p)′>0and at least one n_(p)′ is linked to a neighboring nucleotide viaphosphorothioate linkage, and the sense strand is conjugated to one ormore GalNAc derivatives attached through a bivalent or trivalentbranched linker (described below). In another embodiment, when the RNAiagent is represented by formula (IIId), the N_(a) modifications are2′-O-methyl or 2′-fluoro modifications, n_(p)′>0 and at least one n_(p)′is linked to a neighboring nucleotide via phosphorothioate linkage, thesense strand comprises at least one phosphorothioate linkage, and thesense strand is conjugated to one or more GalNAc derivatives attachedthrough a bivalent or trivalent branched linker.

In one embodiment, when the RNAi agent is represented by formula (IIIa),the N_(a) modifications are 2′-O-methyl or 2′-fluoro modifications,n_(p)′>0 and at least one n_(p)′ is linked to a neighboring nucleotidevia phosphorothioate linkage, the sense strand comprises at least onephosphorothioate linkage, and the sense strand is conjugated to one ormore GalNAc derivatives attached through a bivalent or trivalentbranched linker.

In one embodiment, the RNAi agent is a multimer containing at least twoduplexes represented by formula (III), (IIIa), (IIIb), (IIIc), and(IIId), wherein the duplexes are connected by a linker. The linker canbe cleavable or non-cleavable. Optionally, the multimer furthercomprises a ligand. Each of the duplexes can target the same gene or twodifferent genes; or each of the duplexes can target same gene at twodifferent target sites.

In one embodiment, the RNAi agent is a multimer containing three, four,five, six or more duplexes represented by formula (III), (IIIa), (IIIb),(IIIc), and (IIId), wherein the duplexes are connected by a linker. Thelinker can be cleavable or non-cleavable. Optionally, the multimerfurther comprises a ligand. Each of the duplexes can target the samegene or two different genes; or each of the duplexes can target samegene at two different target sites.

In one embodiment, two RNAi agents represented by formula (III), (IIIa),(IIIb), (IIIc), and (IIId) are linked to each other at the 5′ end, andone or both of the 3′ ends and are optionally conjugated to a ligand.Each of the agents can target the same gene or two different genes; oreach of the agents can target same gene at two different target sites.

Various publications describe multimeric RNAi agents that can be used inthe methods of the invention. Such publications include WO2007/091269,U.S. Pat. No. 7,858,769, WO2010/141511, WO2007/117686, WO2009/014887 andWO2011/031520 the entire contents of each of which are herebyincorporated herein by reference.

As described in more detail below, the RNAi agent that containsconjugations of one or more carbohydrate moieties to a RNAi agent canoptimize one or more properties of the RNAi agent. In many cases, thecarbohydrate moiety will be attached to a modified subunit of the RNAiagent. For example, the ribose sugar of one or more ribonucleotidesubunits of a dsRNA agent can be replaced with another moiety, e.g., anon-carbohydrate (preferably cyclic) carrier to which is attached acarbohydrate ligand. A ribonucleotide subunit in which the ribose sugarof the subunit has been so replaced is referred to herein as a ribosereplacement modification subunit (RRMS). A cyclic carrier may be acarbocyclic ring system, i.e., all ring atoms are carbon atoms, or aheterocyclic ring system, i.e., one or more ring atoms may be aheteroatom, e.g., nitrogen, oxygen, sulfur. The cyclic carrier may be amonocyclic ring system, or may contain two or more rings, e.g. fusedrings. The cyclic carrier may be a fully saturated ring system, or itmay contain one or more double bonds.

The ligand may be attached to the polynucleotide via a carrier. Thecarriers include (i) at least one “backbone attachment point,”preferably two “backbone attachment points” and (ii) at least one“tethering attachment point.” A “backbone attachment point” as usedherein refers to a functional group, e.g. a hydroxyl group, orgenerally, a bond available for, and that is suitable for incorporationof the carrier into the backbone, e.g., the phosphate, or modifiedphosphate, e.g., sulfur containing, backbone, of a ribonucleic acid. A“tethering attachment point” (TAP) in some embodiments refers to aconstituent ring atom of the cyclic carrier, e.g., a carbon atom or aheteroatom (distinct from an atom which provides a backbone attachmentpoint), that connects a selected moiety. The moiety can be, e.g., acarbohydrate, e.g. monosaccharide, disaccharide, trisaccharide,tetrasaccharide, oligosaccharide and polysaccharide. Optionally, theselected moiety is connected by an intervening tether to the cycliccarrier. Thus, the cyclic carrier will often include a functional group,e.g., an amino group, or generally, provide a bond, that is suitable forincorporation or tethering of another chemical entity, e.g., a ligand tothe constituent ring.

The RNAi agents may be conjugated to a ligand via a carrier, wherein thecarrier can be cyclic group or acyclic group; preferably, the cyclicgroup is selected from pyrrolidinyl, pyrazolinyl, pyrazolidinyl,imidazolinyl, imidazolidinyl, piperidinyl, piperazinyl, [1,3]dioxolane,oxazolidinyl, isoxazolidinyl, morpholinyl, thiazolidinyl,isothiazolidinyl, quinoxalinyl, pyridazinonyl, tetrahydrofuryl anddecalin; preferably, the acyclic group is selected from serinol backboneor diethanolamine backbone.

In certain specific embodiments, the RNAi agent for use in the methodsof the invention is an agent selected from the group of agents listed inany one of Tables 3, 4, 5, 6, 18, 19, 20, 21, and 23. These agents mayfurther comprise a ligand.

IV. iRNAs Conjugated to Ligands

Another modification of the RNA of an iRNA suitable for use in themethods of the invention involves chemically linking to the RNA one ormore ligands, moieties or conjugates that enhance the activity, cellulardistribution or cellular uptake of the iRNA. Such moieties include butare not limited to lipid moieties such as a cholesterol moiety(Letsinger et al., Proc. Natl. Acid. Sci. USA, 1989, 86: 6553-6556),cholic acid (Manoharan et al., Biorg. Med. Chem. Let., 1994,4:1053-1060), a thioether, e.g., beryl-S-tritylthiol (Manoharan et al.,Ann. N.Y. Acad. Sci., 1992, 660:306-309; Manoharan et al., Biorg. Med.Chem. Let., 1993, 3:2765-2770), a thiocholesterol (Oberhauser et al.,Nucl. Acids Res., 1992, 20:533-538), an aliphatic chain, e.g.,dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J, 1991,10:1111-1118; Kabanov et al., FEBS Lett., 1990, 259:327-330; Svinarchuket al., Biochimie, 1993, 75:49-54), a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethyl-ammonium1,2-di-O-hexadecyl-rac-glycero-3-phosphonate (Manoharan et al.,Tetrahedron Lett., 1995, 36:3651-3654; Shea et al., Nucl. Acids Res.,1990, 18:3777-3783), a polyamine or a polyethylene glycol chain(Manoharan et al., Nucleosides & Nucleotides, 1995, 14:969-973), oradamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995,36:3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta,1995, 1264:229-237), or an octadecylamine orhexylamino-carbonyloxycholesterol moiety (Crooke et al., J. Pharmacol.Exp. Ther., 1996, 277:923-937).

In one embodiment, a ligand alters the distribution, targeting orlifetime of an iRNA agent into which it is incorporated. In preferredembodiments a ligand provides an enhanced affinity for a selectedtarget, e.g., molecule, cell or cell type, compartment, e.g., a cellularor organ compartment, tissue, organ or region of the body, as, e.g.,compared to a species absent such a ligand. Preferred ligands will nottake part in duplex pairing in a duplexed nucleic acid.

Ligands can include a naturally occurring substance, such as a protein(e.g., human serum albumin (HSA), low-density lipoprotein (LDL), orglobulin); carbohydrate (e.g., a dextran, pullulan, chitin, chitosan,inulin, cyclodextrin, N-acetylgalactosamine, or hyaluronic acid); or alipid. The ligand can also be a recombinant or synthetic molecule, suchas a synthetic polymer, e.g., a synthetic polyamino acid. Examples ofpolyamino acids include polyamino acid is a polylysine (PLL), polyL-aspartic acid, poly L-glutamic acid, styrene-maleic acid anhydridecopolymer, poly(L-lactide-co-glycolide) copolymer, divinyl ether-maleicanhydride copolymer, N-(2-hydroxypropyl)methacrylamide copolymer (HMPA),polyethylene glycol (PEG), polyvinyl alcohol (PVA), polyurethane,poly(2-ethylacrylic acid), N-isopropylacrylamide polymers, orpolyphosphazene. Example of polyamines include: polyethylenimine,polylysine (PLL), spermine, spermidine, polyamine,pseudopeptide-polyamine, peptidomimetic polyamine, dendrimer polyamine,arginine, amidine, protamine, cationic lipid, cationic porphyrin,quaternary salt of a polyamine, or an alpha helical peptide.

Ligands can also include targeting groups, e.g., a cell or tissuetargeting agent, e.g., a lectin, glycoprotein, lipid or protein, e.g.,an antibody, that binds to a specified cell type such as a kidney cell.A targeting group can be a thyrotropin, melanotropin, lectin,glycoprotein, surfactant protein A, Mucin carbohydrate, multivalentlactose, monovalent or multivalent galactose, N-acetyl-galactosamine,N-acetyl-glucosamine multivalent mannose, multivalent fucose,glycosylated polyaminoacids, transferrin, bisphosphonate, polyglutamate,polyaspartate, a lipid, cholesterol, a steroid, bile acid, folate,vitamin B12, vitamin A, biotin, or an RGD peptide or RGD peptidemimetic. In certain embodiments, ligands include monovalent ormultivalent galactose. In certain embodiments, ligands includecholesterol.

Other examples of ligands include dyes, intercalating agents (e.g.acridines), cross-linkers (e.g. psoralen, mitomycin C), porphyrins(TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons (e.g.,phenazine, dihydrophenazine), artificial endonucleases (e.g. EDTA),lipophilic molecules, e.g., cholesterol, cholic acid, adamantane aceticacid, 1-pyrene butyric acid, dihydrotestosterone,1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol,borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid,myristic acid, O3-(oleoyl)lithocholic acid, 03-(oleoyl)cholenic acid,dimethoxytrityl, or phenoxazine) and peptide conjugates (e.g.,antennapedia peptide, Tat peptide), alkylating agents, phosphate, amino,mercapto, PEG (e.g., PEG-40K), MPEG, [MPEG]², polyamino, alkyl,substituted alkyl, radiolabeled markers, enzymes, haptens (e.g. biotin),transport/absorption facilitators (e.g., aspirin, vitamin E, folicacid), synthetic ribonucleases (e.g., imidazole, bisimidazole,histamine, imidazole clusters, acridine-imidazole conjugates, Eu3+complexes of tetraazamacrocycles), dinitrophenyl, HRP, or AP.

Ligands can be proteins, e.g., glycoproteins, or peptides, e.g.,molecules having a specific affinity for a co-ligand, or antibodiese.g., an antibody, that binds to a specified cell type such as a hepaticcell. Ligands can also include hormones and hormone receptors. They canalso include non-peptidic species, such as lipids, lectins,carbohydrates, vitamins, cofactors, multivalent lactose, multivalentgalactose, N-acetyl-galactosamine, N-acetyl-glucosamine multivalentmannose, or multivalent fucose. The ligand can be, for example, alipopolysaccharide, an activator of p38 MAP kinase, or an activator ofNF-κB.

The ligand can be a substance, e.g., a drug, which can increase theuptake of the iRNA agent into the cell, for example, by disrupting thecell's cytoskeleton, e.g., by disrupting the cell's microtubules,microfilaments, and/or intermediate filaments. The drug can be, forexample, taxon, vincristine, vinblastine, cytochalasin, nocodazole,japlakinolide, latrunculin A, phalloidin, swinholide A, indanocine, ormyoservin.

In some embodiments, a ligand attached to an iRNA as described hereinacts as a pharmacokinetic modulator (PK modulator). PK modulatorsinclude lipophiles, bile acids, steroids, phospholipid analogues,peptides, protein binding agents, PEG, vitamins etc. Exemplary PKmodulators include, but are not limited to, cholesterol, fatty acids,cholic acid, lithocholic acid, dialkylglycerides, diacylglyceride,phospholipids, sphingolipids, naproxen, ibuprofen, vitamin E, biotinetc. Oligonucleotides that comprise a number of phosphorothioatelinkages are also known to bind to serum protein, thus shortoligonucleotides, e.g., oligonucleotides of about 5 bases, 10 bases, 15bases or 20 bases, comprising multiple of phosphorothioate linkages inthe backbone are also amenable to the present invention as ligands (e.g.as PK modulating ligands). In addition, aptamers that bind serumcomponents (e.g. serum proteins) are also suitable for use as PKmodulating ligands in the embodiments described herein.

Ligand-conjugated oligonucleotides of the invention may be synthesizedby the use of an oligonucleotide that bears a pendant reactivefunctionality, such as that derived from the attachment of a linkingmolecule onto the oligonucleotide (described below). This reactiveoligonucleotide may be reacted directly with commercially-availableligands, ligands that are synthesized bearing any of a variety ofprotecting groups, or ligands that have a linking moiety attachedthereto.

The oligonucleotides used in the conjugates of the present invention maybe conveniently and routinely made through the well-known technique ofsolid-phase synthesis. Equipment for such synthesis is sold by severalvendors including, for example, Applied Biosystems (Foster City,Calif.). Any other means for such synthesis known in the art mayadditionally or alternatively be employed. It is also known to usesimilar techniques to prepare other oligonucleotides, such as thephosphorothioates and alkylated derivatives.

In the ligand-conjugated oligonucleotides and ligand-molecule bearingsequence-specific linked nucleosides of the present invention, theoligonucleotides and oligonucleosides may be assembled on a suitable DNAsynthesizer utilizing standard nucleotide or nucleoside precursors, ornucleotide or nucleoside conjugate precursors that already bear thelinking moiety, ligand-nucleotide or nucleoside-conjugate precursorsthat already bear the ligand molecule, or non-nucleoside ligand-bearingbuilding blocks.

When using nucleotide-conjugate precursors that already bear a linkingmoiety, the synthesis of the sequence-specific linked nucleosides istypically completed, and the ligand molecule is then reacted with thelinking moiety to form the ligand-conjugated oligonucleotide. In someembodiments, the oligonucleotides or linked nucleosides of the presentinvention are synthesized by an automated synthesizer usingphosphoramidites derived from ligand-nucleoside conjugates in additionto the standard phosphoramidites and non-standard phosphoramidites thatare commercially available and routinely used in oligonucleotidesynthesis.

A. Lipid Conjugates

In one embodiment, the ligand or conjugate is a lipid or lipid-basedmolecule. Such a lipid or lipid-based molecule preferably binds a serumprotein, e.g., human serum albumin (HSA). An HSA binding ligand allowsfor distribution of the conjugate to a target tissue, e.g., a non-kidneytarget tissue of the body. For example, the target tissue can be theliver, including parenchymal cells of the liver. Other molecules thatcan bind HSA can also be used as ligands. For example, naproxen oraspirin can be used. A lipid or lipid-based ligand can (a) increaseresistance to degradation of the conjugate, (b) increase targeting ortransport into a target cell or cell membrane, and/or (c) can be used toadjust binding to a serum protein, e.g., HSA.

A lipid based ligand can be used to inhibit, e.g., control the bindingof the conjugate to a target tissue. For example, a lipid or lipid-basedligand that binds to HSA more strongly will be less likely to betargeted to the kidney and therefore less likely to be cleared from thebody. A lipid or lipid-based ligand that binds to HSA less strongly canbe used to target the conjugate to the kidney.

In a preferred embodiment, the lipid based ligand binds HSA. Preferably,it binds HSA with a sufficient affinity such that the conjugate will bepreferably distributed to a non-kidney tissue. However, it is preferredthat the affinity not be so strong that the HSA-ligand binding cannot bereversed.

In another preferred embodiment, the lipid based ligand binds HSA weaklyor not at all, such that the conjugate will be preferably distributed tothe kidney. Other moieties that target to kidney cells can also be usedin place of or in addition to the lipid based ligand.

In another aspect, the ligand is a moiety, e.g., a vitamin, which istaken up by a target cell, e.g., a proliferating cell. These areparticularly useful for treating disorders characterized by unwantedcell proliferation, e.g., of the malignant or non-malignant type, e.g.,cancer cells. Exemplary vitamins include vitamin A, E, and K. Otherexemplary vitamins include are B vitamin, e.g., folic acid, B12,riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up bytarget cells such as liver cells. Also included are HSA and low densitylipoprotein (LDL).

B. Cell Permeation Agents

In another aspect, the ligand is a cell-permeation agent, preferably ahelical cell-permeation agent. Preferably, the agent is amphipathic. Anexemplary agent is a peptide such as tat or antennapedia. If the agentis a peptide, it can be modified, including a peptidylmimetic,invertomers, non-peptide or pseudo-peptide linkages, and use of D-aminoacids. The helical agent is preferably an alpha-helical agent, whichpreferably has a lipophilic and a lipophobic phase.

The ligand can be a peptide or peptidomimetic. A peptidomimetic (alsoreferred to herein as an oligopeptidomimetic) is a molecule capable offolding into a defined three-dimensional structure similar to a naturalpeptide. The attachment of peptide and peptidomimetics to iRNA agentscan affect pharmacokinetic distribution of the iRNA, such as byenhancing cellular recognition and absorption. The peptide orpeptidomimetic moiety can be about 5-50 amino acids long, e.g., about 5,10, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids long.

A peptide or peptidomimetic can be, for example, a cell permeationpeptide, cationic peptide, amphipathic peptide, or hydrophobic peptide(e.g., consisting primarily of Tyr, Trp or Phe). The peptide moiety canbe a dendrimer peptide, constrained peptide or crosslinked peptide. Inanother alternative, the peptide moiety can include a hydrophobicmembrane translocation sequence (MTS). An exemplary hydrophobicMTS-containing peptide is RFGF having the amino acid sequenceAAVALLPAVLLALLAP (SEQ ID NO: 3). An RFGF analogue (e.g., amino acidsequence AALLPVLLAAP (SEQ ID NO: 4) containing a hydrophobic MTS canalso be a targeting moiety. The peptide moiety can be a “delivery”peptide, which can carry large polar molecules including peptides,oligonucleotides, and protein across cell membranes. For example,sequences from the HIV Tat protein (GRKKRRQRRRPPQ (SEQ ID NO: 5) and theDrosophila Antennapedia protein (RQIKIWFQNRRMKWKK (SEQ ID NO: 6) havebeen found to be capable of functioning as delivery peptides. A peptideor peptidomimetic can be encoded by a random sequence of DNA, such as apeptide identified from a phage-display library, orone-bead-one-compound (OBOC) combinatorial library (Lam et al., Nature,354:82-84, 1991). Examples of a peptide or peptidomimetic tethered to adsRNA agent via an incorporated monomer unit for cell targeting purposesis an arginine-glycine-aspartic acid (RGD)-peptide, or RGD mimic. Apeptide moiety can range in length from about 5 amino acids to about 40amino acids. The peptide moieties can have a structural modification,such as to increase stability or direct conformational properties. Anyof the structural modifications described below can be utilized.

An RGD peptide for use in the compositions and methods of the inventionmay be linear or cyclic, and may be modified, e.g., glycosylated ormethylated, to facilitate targeting to a specific tissue(s).RGD-containing peptides and peptidomimetics may include D-amino acids,as well as synthetic RGD mimics. In addition to RGD, one can use othermoieties that target the integrin ligand. Preferred conjugates of thisligand target PECAM-1 or VEGF.

A “cell permeation peptide” is capable of permeating a cell, e.g., amicrobial cell, such as a bacterial or fungal cell, or a mammalian cell,such as a human cell. A microbial cell-permeating peptide can be, forexample, a α-helical linear peptide (e.g., LL-37 or Ceropin P1), adisulfide bond-containing peptide (e.g., α-defensin, β-defensin orbactenecin), or a peptide containing only one or two dominating aminoacids (e.g., PR-39 or indolicidin). A cell permeation peptide can alsoinclude a nuclear localization signal (NLS). For example, a cellpermeation peptide can be a bipartite amphipathic peptide, such as MPG,which is derived from the fusion peptide domain of HIV-1 gp41 and theNLS of SV40 large T antigen (Simeoni et al., Nucl. Acids Res.31:2717-2724, 2003).

C. Carbohydrate Conjugates

In some embodiments of the compositions and methods of the invention, aniRNA oligonucleotide further comprises a carbohydrate. The carbohydrateconjugated iRNA are advantageous for the in vivo delivery of nucleicacids, as well as compositions suitable for in vivo therapeutic use, asdescribed herein. As used herein, “carbohydrate” refers to a compoundwhich is either a carbohydrate per se made up of one or moremonosaccharide units having at least 6 carbon atoms (which can belinear, branched or cyclic) with an oxygen, nitrogen or sulfur atombonded to each carbon atom; or a compound having as a part thereof acarbohydrate moiety made up of one or more monosaccharide units eachhaving at least six carbon atoms (which can be linear, branched orcyclic), with an oxygen, nitrogen or sulfur atom bonded to each carbonatom. Representative carbohydrates include the sugars (mono-, di-, tri-and oligosaccharides containing from about 4, 5, 6, 7, 8, or 9monosaccharide units), and polysaccharides such as starches, glycogen,cellulose and polysaccharide gums. Specific monosaccharides include C5and above (e.g., C5, C6, C7, or C8) sugars; di- and trisaccharidesinclude sugars having two or three monosaccharide units (e.g., C5, C6,C7, or C8).

In one embodiment, a carbohydrate conjugate for use in the compositionsand methods of the invention is a monosaccharide. In another embodiment,a carbohydrate conjugate for use in the compositions and methods of theinvention is selected from the group consisting of:

In one embodiment, the monosaccharide is an N-acetylgalactosamine, suchas

Another representative carbohydrate conjugate for use in the embodimentsdescribed herein includes, but is not limited to,

(Formula XXIII), when one of X or Y is an oligonucleotide, the other isa hydrogen.

In certain embodiments of the invention, the GalNAc or GalNAc derivativeis attached to an iRNA agent of the invention via a monovalent linker.In some embodiments, the GalNAc or GalNAc derivative is attached to aniRNA agent of the invention via a bivalent linker. In yet otherembodiments of the invention, the GalNAc or GalNAc derivative isattached to an iRNA agent of the invention via a trivalent linker.

In one embodiment, the double stranded RNAi agents of the inventioncomprise one GalNAc or GalNAc derivative attached to the iRNA agent. Inanother embodiment, the double stranded RNAi agents of the inventioncomprise a plurality (e.g., 2, 3, 4, 5, or 6) GalNAc or GalNAcderivatives, each independently attached to a plurality of nucleotidesof the double stranded RNAi agent through a plurality of monovalentlinkers.

In some embodiments, for example, when the two strands of an iRNA agentof the invention are part of one larger molecule connected by anuninterrupted chain of nucleotides between the 3′-end of one strand andthe 5′-end of the respective other strand forming a hairpin loopcomprising, a plurality of unpaired nucleotides, each unpairednucleotide within the hairpin loop may independently comprise a GalNAcor GalNAc derivative attached via a monovalent linker. The hairpin loopmay also be formed by an extended overhang in one strand of the duplex.

In some embodiments, the carbohydrate conjugate further comprises one ormore additional ligands as described above, such as, but not limited to,a PK modulator and/or a cell permeation peptide.

Additional carbohydrate conjugates suitable for use in the presentinvention include those described in PCT Publication Nos. WO 2014/179620and WO 2014/179627, the entire contents of each of which areincorporated herein by reference.

D. Linkers

In some embodiments, the conjugate or ligand described herein can beattached to an iRNA oligonucleotide with various linkers that can becleavable or non-cleavable.

The term “linker” or “linking group” means an organic moiety thatconnects two parts of a compound, e.g., covalently attaches two parts ofa compound. Linkers typically comprise a direct bond or an atom such asoxygen or sulfur, a unit such as NR8, C(O), C(O)NH, SO, SO₂, SO₂NH or achain of atoms, such as, but not limited to, substituted orunsubstituted alkyl, substituted or unsubstituted alkenyl, substitutedor unsubstituted alkynyl, arylalkyl, arylalkenyl, arylalkynyl,heteroarylalkyl, heteroarylalkenyl, heteroarylalkynyl,heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, aryl,heteroaryl, heterocyclyl, cycloalkyl, cycloalkenyl, alkylarylalkyl,alkylarylalkenyl, alkylarylalkynyl, alkenylarylalkyl,alkenylarylalkenyl, alkenylarylalkynyl, alkynylarylalkyl,alkynylarylalkenyl, alkynylarylalkynyl, alkylheteroarylalkyl,alkylheteroarylalkenyl, alkylheteroarylalkynyl, alkenylheteroarylalkyl,alkenylheteroarylalkenyl, alkenylheteroarylalkynyl,alkynylheteroarylalkyl, alkynylheteroarylalkenyl,alkynylheteroarylalkynyl, alkylheterocyclylalkyl,alkylheterocyclylalkenyl, alkylhererocyclylalkynyl,alkenylheterocyclylalkyl, alkenylheterocyclylalkenyl,alkenylheterocyclylalkynyl, alkynylheterocyclylalkyl,alkynylheterocyclylalkenyl, alkynylheterocyclylalkynyl, alkylaryl,alkenylaryl, alkynylaryl, alkylheteroaryl, alkenylheteroaryl,alkynylhereroaryl, which one or more methylenes can be interrupted orterminated by O, S, S(O), SO₂, N(R8), C(O), substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heterocyclic; where R8 is hydrogen, acyl, aliphatic orsubstituted aliphatic. In one embodiment, the linker is between about1-24 atoms, 2-24, 3-24, 4-24, 5-24, 6-24, 6-18, 7-18, 8-18 atoms, 7-17,8-17, 6-16, 7-16, or 8-16 atoms.

A cleavable linking group is one which is sufficiently stable outsidethe cell, but which upon entry into a target cell is cleaved to releasethe two parts the linker is holding together. In a preferred embodiment,the cleavable linking group is cleaved at least about 10 times, 20,times, 30 times, 40 times, 50 times, 60 times, 70 times, 80 times, 90times or more, or at least about 100 times faster in a target cell orunder a first reference condition (which can, e.g., be selected to mimicor represent intracellular conditions) than in the blood of a subject,or under a second reference condition (which can, e.g., be selected tomimic or represent conditions found in the blood or serum).

Cleavable linking groups are susceptible to cleavage agents, e.g., pH,redox potential or the presence of degradative molecules. Generally,cleavage agents are more prevalent or found at higher levels oractivities inside cells than in serum or blood. Examples of suchdegradative agents include: redox agents which are selected forparticular substrates or which have no substrate specificity, including,e.g., oxidative or reductive enzymes or reductive agents such asmercaptans, present in cells, that can degrade a redox cleavable linkinggroup by reduction; esterases; endosomes or agents that can create anacidic environment, e.g., those that result in a pH of five or lower;enzymes that can hydrolyze or degrade an acid cleavable linking group byacting as a general acid, peptidases (which can be substrate specific),and phosphatases.

A cleavable linkage group, such as a disulfide bond can be susceptibleto pH. The pH of human serum is 7.4, while the average intracellular pHis slightly lower, ranging from about 7.1-7.3. Endosomes have a moreacidic pH, in the range of 5.5-6.0, and lysosomes have an even moreacidic pH at around 5.0. Some linkers will have a cleavable linkinggroup that is cleaved at a preferred pH, thereby releasing a cationiclipid from the ligand inside the cell, or into the desired compartmentof the cell.

A linker can include a cleavable linking group that is cleavable by aparticular enzyme. The type of cleavable linking group incorporated intoa linker can depend on the cell to be targeted. For example, aliver-targeting ligand can be linked to a cationic lipid through alinker that includes an ester group. Liver cells are rich in esterases,and therefore the linker will be cleaved more efficiently in liver cellsthan in cell types that are not esterase-rich. Other cell-types rich inesterases include cells of the lung, renal cortex, and testis.

Linkers that contain peptide bonds can be used when targeting cell typesrich in peptidases, such as liver cells and synoviocytes.

In general, the suitability of a candidate cleavable linking group canbe evaluated by testing the ability of a degradative agent (orcondition) to cleave the candidate linking group. It will also bedesirable to also test the candidate cleavable linking group for theability to resist cleavage in the blood or when in contact with othernon-target tissue. Thus, one can determine the relative susceptibilityto cleavage between a first and a second condition, where the first isselected to be indicative of cleavage in a target cell and the second isselected to be indicative of cleavage in other tissues or biologicalfluids, e.g., blood or serum. The evaluations can be carried out in cellfree systems, in cells, in cell culture, in organ or tissue culture, orin whole animals. It can be useful to make initial evaluations incell-free or culture conditions and to confirm by further evaluations inwhole animals. In preferred embodiments, useful candidate compounds arecleaved at least about 2, 4, 10, 20, 30, 40, 50, 60, 70, 80, 90, orabout 100 times faster in the cell (or under in vitro conditionsselected to mimic intracellular conditions) as compared to blood orserum (or under in vitro conditions selected to mimic extracellularconditions).

i. Redox Cleavable Linking Groups

In one embodiment, a cleavable linking group is a redox cleavablelinking group that is cleaved upon reduction or oxidation. An example ofreductively cleavable linking group is a disulphide linking group(—S—S—). To determine if a candidate cleavable linking group is asuitable “reductively cleavable linking group,” or for example issuitable for use with a particular iRNA moiety and particular targetingagent one can look to methods described herein. For example, a candidatecan be evaluated by incubation with dithiothreitol (DTT), or otherreducing agent using reagents know in the art, which mimic the rate ofcleavage which would be observed in a cell, e.g., a target cell. Thecandidates can also be evaluated under conditions which are selected tomimic blood or serum conditions. In one, candidate compounds are cleavedby at most about 10% in the blood. In other embodiments, usefulcandidate compounds are degraded at least about 2, 4, 10, 20, 30, 40,50, 60, 70, 80, 90, or about 100 times faster in the cell (or under invitro conditions selected to mimic intracellular conditions) as comparedto blood (or under in vitro conditions selected to mimic extracellularconditions). The rate of cleavage of candidate compounds can bedetermined using standard enzyme kinetics assays under conditions chosento mimic intracellular media and compared to conditions chosen to mimicextracellular media.

ii. Phosphate-Based Cleavable Linking Groups

In another embodiment, a cleavable linker comprises a phosphate-basedcleavable linking group. A phosphate-based cleavable linking group iscleaved by agents that degrade or hydrolyze the phosphate group. Anexample of an agent that cleaves phosphate groups in cells are enzymessuch as phosphatases in cells. Examples of phosphate-based linkinggroups are —O—P(O)(ORk)-O—, —O—P(S)(ORk)-O—, —O—P(S)(SRk)-O—,—S—P(O)(ORk)-O—, —O—P(O)(ORk)-S—, —S—P(O)(ORk)-S—, —O—P(S)(ORk)-S—,—S—P(S)(ORk)-O—, —O—P(O)(Rk)-O—, —O—P(S)(Rk)-O—, —S—P(O)(Rk)-O—,—S—P(S)(Rk)-O—, —S—P(O)(Rk)-S—, —O—P(S)(Rk)-S—. Preferred embodimentsare —O—P(O)(OH)—O—, —O—P(S)(OH)—O—, —O—P(S)(SH)—O—, —S—P(O)(OH)—O—,—O—P(O)(OH)—S—, —S—P(O)(OH)—S—, —O—P(S)(OH)—S—, —S—P(S)(OH)—O—,—O—P(O)(H)—O—, —O—P(S)(H)—O—, —S—P(O)(H)—O, —S—P(S)(H)—O—,—S—P(O)(H)—S—, —O—P(S)(H)—S—. A preferred embodiment is —O—P(O)(OH)—O—.These candidates can be evaluated using methods analogous to thosedescribed above.

iii. Acid Cleavable Linking Groups

In another embodiment, a cleavable linker comprises an acid cleavablelinking group. An acid cleavable linking group is a linking group thatis cleaved under acidic conditions. In preferred embodiments acidcleavable linking groups are cleaved in an acidic environment with a pHof about 6.5 or lower (e.g., about 6.0, 5.75, 5.5, 5.25, 5.0, or lower),or by agents such as enzymes that can act as a general acid. In a cell,specific low pH organelles, such as endosomes and lysosomes can providea cleaving environment for acid cleavable linking groups. Examples ofacid cleavable linking groups include but are not limited to hydrazones,esters, and esters of amino acids. Acid cleavable groups can have thegeneral formula —C═NN—, C(O)O, or —OC(O). A preferred embodiment is whenthe carbon attached to the oxygen of the ester (the alkoxy group) is anaryl group, substituted alkyl group, or tertiary alkyl group such asdimethyl pentyl or t-butyl. These candidates can be evaluated usingmethods analogous to those described above.

iv. Ester-Based Linking Groups

In another embodiment, a cleavable linker comprises an ester-basedcleavable linking group. An ester-based cleavable linking group iscleaved by enzymes such as esterases and amidases in cells. Examples ofester-based cleavable linking groups include but are not limited toesters of alkylene, alkenylene and alkynylene groups. Ester cleavablelinking groups have the general formula —C(O)O—, or —OC(O)—. Thesecandidates can be evaluated using methods analogous to those describedabove.

v. Peptide-Based Cleaving Groups

In yet another embodiment, a cleavable linker comprises a peptide-basedcleavable linking group. A peptide-based cleavable linking group iscleaved by enzymes such as peptidases and proteases in cells.Peptide-based cleavable linking groups are peptide bonds formed betweenamino acids to yield oligopeptides (e.g., dipeptides, tripeptides etc.)and polypeptides. Peptide-based cleavable groups do not include theamide group (—C(O)NH—). The amide group can be formed between anyalkylene, alkenylene or alkynylene. A peptide bond is a special type ofamide bond formed between amino acids to yield peptides and proteins.The peptide based cleavage group is generally limited to the peptidebond (i.e., the amide bond) formed between amino acids yielding peptidesand proteins and does not include the entire amide functional group.Peptide-based cleavable linking groups have the general formula—NHCHRAC(O)NHCHRBC(O)—, where RA and RB are the R groups of the twoadjacent amino acids. These candidates can be evaluated using methodsanalogous to those described above.

In one embodiment, an iRNA of the invention is conjugated to acarbohydrate through a linker. Non-limiting examples of iRNAcarbohydrate conjugates with linkers of the compositions and methods ofthe invention include, but are not limited to,

when one of X or Y is an oligonucleotide, the other is a hydrogen.

In certain embodiments of the compositions and methods of the invention,a ligand is one or more GalNAc (N-acetylgalactosamine) derivativesattached through a bivalent or trivalent branched linker.

In one embodiment, a dsRNA of the invention is conjugated to a bivalentor trivalent branched linker selected from the group of structures shownin any of formula (XXXII)—(XXXV):

wherein:q2A, q2B, q3A, q3B, q4A, q4B, q5A, q5B and q5C represent independentlyfor each occurrence 0-20 and wherein the repeating unit can be the sameor different;p^(2A), p^(2B), p^(3A), p^(3B), p^(4A), p^(4B), p^(5A), p^(5B), p^(5C),T^(2A), T^(2B), T^(3A), T^(3B), T^(4A), T^(4B), T^(4A), T^(5B), T^(5C)are each independently for each occurrence absent, CO, NH, O, S, OC(O),NHC(O), CH₂, CH₂NH or CH₂O;

Q^(2A), Q^(2B), Q^(3A), Q^(3B), Q^(4A), Q^(4B), Q^(5A), Q^(5B), Q^(5C)are independently for each occurrence absent, alkylene, substitutedalkylene wherein one or more methylenes can be interrupted or terminatedby one or more of 0, S, S(O), SO₂, N(R^(N)), C(R′)═C(R″), CC or C(O);

R^(2A), R^(2B), R^(3A), R^(3B), R^(4A), R^(4B), R^(5A), R^(5B), R^(5C)are each independently for each occurrence absent, NH, O, S, CH₂, C(O)O,C(O)NH, NHCH(R^(a))C(O), —C(O)—CH(R^(a))—NH—, CO, CH═N—O,

or heterocyclyl;

L^(2A), L^(2B), L^(3A), L^(3B), L^(4A), L^(4B), L^(5A), L^(5B) andL^(5C) represent the ligand; i.e. each independently for each occurrencea monosaccharide (such as GalNAc), disaccharide, trisaccharide,tetrasaccharide, oligosaccharide, or polysaccharide; and R^(a) is H oramino acid side chain. Trivalent conjugating GalNAc derivatives areparticularly useful for use with RNAi agents for inhibiting theexpression of a target gene, such as those of formula (XXXVI):

wherein L^(5A), L^(5B) and L^(5C) represent a monosaccharide, such asGalNAc derivative.

Examples of suitable bivalent and trivalent branched linker groupsconjugating GalNAc derivatives include, but are not limited to, thestructures recited above as formulas II, VII, XI, X, and XIII.

Representative U.S. patents that teach the preparation of RNA conjugatesinclude, but are not limited to, U.S. Pat. Nos. 4,828,979; 4,948,882;5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717,5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077;5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735;4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335;4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830;5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536;5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203,5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810;5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923;5,599,928 and 5,688,941; 6,294,664; 6,320,017; 6,576,752; 6,783,931;6,900,297; 7,037,646; 8,106,022, the entire contents of each of whichare hereby incorporated herein by reference.

It is not necessary for all positions in a given compound to beuniformly modified, and in fact more than one of the aforementionedmodifications can be incorporated in a single compound or even at asingle nucleoside within an iRNA. The present invention also includesiRNA compounds that are chimeric compounds.

“Chimeric” iRNA compounds or “chimeras,” in the context of thisinvention, are iRNA compounds, preferably dsRNAs, which contain two ormore chemically distinct regions, each made up of at least one monomerunit, i.e., a nucleotide in the case of a dsRNA compound. These iRNAstypically contain at least one region wherein the RNA is modified so asto confer upon the iRNA increased resistance to nuclease degradation,increased cellular uptake, and/or increased binding affinity for thetarget nucleic acid. An additional region of the iRNA can serve as asubstrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. Byway of example, RNase H is a cellular endonuclease which cleaves the RNAstrand of an RNA:DNA duplex. Activation of RNase H, therefore, resultsin cleavage of the RNA target, thereby greatly enhancing the efficiencyof iRNA inhibition of gene expression. Consequently, comparable resultscan often be obtained with shorter iRNAs when chimeric dsRNAs are used,compared to phosphorothioate deoxy dsRNAs hybridizing to the same targetregion. Cleavage of the RNA target can be routinely detected by gelelectrophoresis and, if necessary, associated nucleic acid hybridizationtechniques known in the art.

In certain instances, the RNA of an iRNA can be modified by a non-ligandgroup. A number of non-ligand molecules have been conjugated to iRNAs inorder to enhance the activity, cellular distribution or cellular uptakeof the iRNA, and procedures for performing such conjugations areavailable in the scientific literature. Such non-ligand moieties haveincluded lipid moieties, such as cholesterol (Kubo, T. et al., Biochem.Biophys. Res. Comm., 2007, 365(1):54-61; Letsinger et al., Proc. Natl.Acad. Sci. USA, 1989, 86:6553), cholic acid (Manoharan et al., Bioorg.Med. Chem. Lett., 1994, 4:1053), a thioether, e.g., hexyl-S-tritylthiol(Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660:306; Manoharan etal., Bioorg. Med. Chem. Let., 1993, 3:2765), a thiocholesterol(Oberhauser et al., Nucl. Acids Res., 1992, 20:533), an aliphatic chain,e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J.,1991, 10:111; Kabanov et al., FEBS Lett., 1990, 259:327; Svinarchuk etal., Biochimie, 1993, 75:49), a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al.,Tetrahedron Lett., 1995, 36:3651; Shea et al., Nucl. Acids Res., 1990,18:3777), a polyamine or a polyethylene glycol chain (Manoharan et al.,Nucleosides & Nucleotides, 1995, 14:969), or adamantane acetic acid(Manoharan et al., Tetrahedron Lett., 1995, 36:3651), a palmityl moiety(Mishra et al., Biochim. Biophys. Acta, 1995, 1264:229), or anoctadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke etal., J. Pharmacol. Exp. Ther., 1996, 277:923). Representative UnitedStates patents that teach the preparation of such RNA conjugates havebeen listed above. Typical conjugation protocols involve the synthesisof an RNAs bearing an aminolinker at one or more positions of thesequence. The amino group is then reacted with the molecule beingconjugated using appropriate coupling or activating reagents. Theconjugation reaction can be performed either with the RNA still bound tothe solid support or following cleavage of the RNA, in solution phase.Purification of the RNA conjugate by HPLC typically affords the pureconjugate.

IV. Delivery of an iRNA of the Invention

The delivery of an iRNA of the invention to a cell e.g., a cell within asubject, such as a human subject (e.g., a subject in need thereof, suchas a subject having a disorder that would benefit from reduction inPCSK9 expression) can be achieved in a number of different ways. Forexample, delivery may be performed by contacting a cell with an iRNA ofthe invention either in vitro or in vivo. In vivo delivery may also beperformed directly by administering a composition comprising an iRNA,e.g., a dsRNA, to a subject. Alternatively, in vivo delivery may beperformed indirectly by administering one or more vectors that encodeand direct the expression of the iRNA. These alternatives are discussedfurther below.

In general, any method of delivering a nucleic acid molecule (in vitroor in vivo) can be adapted for use with an iRNA of the invention (seee.g., Akhtar S. and Julian R L. (1992) Trends Cell. Biol. 2(5):139-144and WO94/02595, which are incorporated herein by reference in theirentireties). For in vivo delivery, factors to consider in order todeliver an iRNA molecule include, for example, biological stability ofthe delivered molecule, prevention of non-specific effects, andaccumulation of the delivered molecule in the target tissue. Thenon-specific effects of an iRNA can be minimized by localadministration, for example, by direct injection or implantation into atissue or topically administering the preparation. Local administrationto a treatment site maximizes local concentration of the agent, limitsthe exposure of the agent to systemic tissues that can otherwise beharmed by the agent or that can degrade the agent, and permits a lowertotal dose of the iRNA molecule to be administered. Several studies haveshown successful knockdown of gene products when an iRNA is administeredlocally. For example, intraocular delivery of a VEGF dsRNA byintravitreal injection in cynomolgus monkeys (Tolentino, M J., et al(2004) Retina 24:132-138) and subretinal injections in mice (Reich, SJ., et al (2003) Mol. Vis. 9:210-216) were both shown to preventneovascularization in an experimental model of age-related maculardegeneration. In addition, direct intratumoral injection of a dsRNA inmice reduces tumor volume (Pille, J., et al (2005) Mol. Ther.11:267-274) and can prolong survival of tumor-bearing mice (Kim, W J.,et al (2006) Mol. Ther. 14:343-350; Li, S., et al (2007) Mol. Ther.15:515-523). RNA interference has also shown success with local deliveryto the CNS by direct injection (Dorn, G., et al. (2004) Nucleic Acids32:e49; Tan, P H., et al (2005) Gene Ther. 12:59-66; Makimura, H., et al(2002) BMC Neurosci. 3:18; Shishkina, G T., et al (2004) Neuroscience129:521-528; Thakker, E R., et al (2004) Proc. Natl. Acad. Sci. U.S.A.101:17270-17275; Akaneya, Y., et al (2005) J. Neurophysiol. 93:594-602)and to the lungs by intranasal administration (Howard, K A., et al(2006) Mol. Ther. 14:476-484; Zhang, X., et al (2004) J. Biol. Chem.279:10677-10684; Bitko, V., et al (2005) Nat. Med. 11:50-55). Foradministering an iRNA systemically for the treatment of a disease, theRNA can be modified or alternatively delivered using a drug deliverysystem; both methods act to prevent the rapid degradation of the dsRNAby endo- and exo-nucleases in vivo. Modification of the RNA or thepharmaceutical carrier can also permit targeting of the iRNA compositionto the target tissue and avoid undesirable off-target effects. iRNAmolecules can be modified by chemical conjugation to lipophilic groupssuch as cholesterol to enhance cellular uptake and prevent degradation.For example, an iRNA directed against ApoB conjugated to a lipophiliccholesterol moiety was injected systemically into mice and resulted inknockdown of apoB mRNA in both the liver and jejunum (Soutschek, J., etal (2004) Nature 432:173-178). Conjugation of an iRNA to an aptamer hasbeen shown to inhibit tumor growth and mediate tumor regression in amouse model of prostate cancer (McNamara, J O., et al (2006) Nat.Biotechnol. 24:1005-1015). In an alternative embodiment, the iRNA can bedelivered using drug delivery systems such as a nanoparticle, adendrimer, a polymer, liposomes, or a cationic delivery system.Positively charged cationic delivery systems facilitate binding of aniRNA molecule (negatively charged) and also enhance interactions at thenegatively charged cell membrane to permit efficient uptake of an iRNAby the cell. Cationic lipids, dendrimers, or polymers can either bebound to an iRNA, or induced to form a vesicle or micelle (see e.g., KimS H., et al (2008) Journal of Controlled Release 129(2):107-116) thatencases an iRNA. The formation of vesicles or micelles further preventsdegradation of the iRNA when administered systemically. Methods formaking and administering cationic-iRNA complexes are well within theabilities of one skilled in the art (see e.g., Sorensen, D R., et al(2003) J. Mol. Biol 327:761-766; Verma, U N., et al (2003) Clin. CancerRes. 9:1291-1300; Arnold, A S et al (2007) J. Hypertens. 25:197-205,which are incorporated herein by reference in their entirety). Somenon-limiting examples of drug delivery systems useful for systemicdelivery of iRNAs include DOTAP (Sorensen, D R., et al (2003), supra;Verma, U N., et al (2003), supra), Oligofectamine, “solid nucleic acidlipid particles” (Zimmermann, T S., et al (2006) Nature 441:111-114),cardiolipin (Chien, P Y., et al (2005) Cancer Gene Ther. 12:321-328;Pal, A., et al (2005) Int J. Oncol. 26:1087-1091), polyethyleneimine(Bonnet M E., et al (2008) Pharm. Res. August 16 Epub ahead of print;Aigner, A. (2006) J. Biomed. Biotechnol. 71659), Arg-Gly-Asp (RGD)peptides (Liu, S. (2006) Mol. Pharm. 3:472-487), and polyamidoamines(Tomalia, D A., et al (2007) Biochem. Soc. Trans. 35:61-67; Yoo, H., etal (1999) Pharm. Res. 16:1799-1804). In some embodiments, an iRNA formsa complex with cyclodextrin for systemic administration. Methods foradministration and pharmaceutical compositions of iRNAs andcyclodextrins can be found in U.S. Pat. No. 7,427,605, which is hereinincorporated by reference in its entirety.

A. Vector Encoded iRNAs of the Invention

iRNA targeting the PCSK9 gene can be expressed from transcription unitsinserted into DNA or RNA vectors (see, e.g., Couture, A, et al., TIG.(1996), 12:5-10; Skillern, A., et al., International PCT Publication No.WO 00/22113, Conrad, International PCT Publication No. WO 00/22114, andConrad, U.S. Pat. No. 6,054,299). Expression can be transient (on theorder of hours to weeks) or sustained (weeks to months or longer),depending upon the specific construct used and the target tissue or celltype. These transgenes can be introduced as a linear construct, acircular plasmid, or a viral vector, which can be an integrating ornon-integrating vector. The transgene can also be constructed to permitit to be inherited as an extrachromosomal plasmid (Gassmann, et al.,Proc. Natl. Acad. Sci. USA (1995) 92:1292).

The individual strand or strands of an iRNA can be transcribed from apromoter on an expression vector. Where two separate strands are to beexpressed to generate, for example, a dsRNA, two separate expressionvectors can be co-introduced (e.g., by transfection or infection) into atarget cell. Alternatively each individual strand of a dsRNA can betranscribed by promoters both of which are located on the sameexpression plasmid. In one embodiment, a dsRNA is expressed as invertedrepeat polynucleotides joined by a linker polynucleotide sequence suchthat the dsRNA has a stem and loop structure.

iRNA expression vectors are generally DNA plasmids or viral vectors.Expression vectors compatible with eukaryotic cells, preferably thosecompatible with vertebrate cells, can be used to produce recombinantconstructs for the expression of an iRNA as described herein. Eukaryoticcell expression vectors are well known in the art and are available froma number of commercial sources. Typically, such vectors are providedcontaining convenient restriction sites for insertion of the desirednucleic acid segment. Delivery of iRNA expressing vectors can besystemic, such as by intravenous or intramuscular administration, byadministration to target cells ex-planted from the patient followed byreintroduction into the patient, or by any other means that allows forintroduction into a desired target cell.

iRNA expression plasmids can be transfected into target cells as acomplex with cationic lipid carriers (e.g., Oligofectamine) ornon-cationic lipid-based carriers (e.g., Transit-TKO™). Multiple lipidtransfections for iRNA-mediated knockdowns targeting different regionsof a target RNA over a period of a week or more are also contemplated bythe invention. Successful introduction of vectors into host cells can bemonitored using various known methods. For example, transienttransfection can be signaled with a reporter, such as a fluorescentmarker, such as Green Fluorescent Protein (GFP). Stable transfection ofcells ex vivo can be ensured using markers that provide the transfectedcell with resistance to specific environmental factors (e.g.,antibiotics and drugs), such as hygromycin B resistance.

Viral vector systems which can be utilized with the methods andcompositions described herein include, but are not limited to, (a)adenovirus vectors; (b) retrovirus vectors, including but not limited tolentiviral vectors, moloney murine leukemia virus, etc.; (c)adeno-associated virus vectors; (d) herpes simplex virus vectors; (e) SV40 vectors; (f) polyoma virus vectors; (g) papilloma virus vectors; (h)picornavirus vectors; (i) pox virus vectors such as an orthopox, e.g.,vaccinia virus vectors or avipox, e.g. canary pox or fowl pox; and (j) ahelper-dependent or gutless adenovirus. Replication-defective virusescan also be advantageous. Different vectors will or will not becomeincorporated into the cells' genome. The constructs can include viralsequences for transfection, if desired. Alternatively, the construct canbe incorporated into vectors capable of episomal replication, e.g. EPVand EBV vectors. Constructs for the recombinant expression of an iRNAwill generally require regulatory elements, e.g., promoters, enhancers,etc., to ensure the expression of the iRNA in target cells. Otheraspects to consider for vectors and constructs are further describedbelow.

Vectors useful for the delivery of an iRNA will include regulatoryelements (promoter, enhancer, etc.) sufficient for expression of theiRNA in the desired target cell or tissue. The regulatory elements canbe chosen to provide either constitutive or regulated/inducibleexpression.

Expression of the iRNA can be precisely regulated, for example, by usingan inducible regulatory sequence that is sensitive to certainphysiological regulators, e.g., circulating glucose levels, or hormones(Docherty et al., 1994, FASEB J. 8:20-24). Such inducible expressionsystems, suitable for the control of dsRNA expression in cells or inmammals include, for example, regulation by ecdysone, by estrogen,progesterone, tetracycline, chemical inducers of dimerization, andisopropyl-beta-D1-thiogalactopyranoside (IPTG). A person skilled in theart would be able to choose the appropriate regulatory/promoter sequencebased on the intended use of the iRNA transgene.

Viral vectors that contain nucleic acid sequences encoding an iRNA canbe used. For example, a retroviral vector can be used (see Miller etal., Meth. Enzymol. 217:581-599 (1993)). These retroviral vectorscontain the components necessary for the correct packaging of the viralgenome and integration into the host cell DNA. The nucleic acidsequences encoding an iRNA are cloned into one or more vectors, whichfacilitate delivery of the nucleic acid into a patient. More detailabout retroviral vectors can be found, for example, in Boesen et al.,Biotherapy 6:291-302 (1994), which describes the use of a retroviralvector to deliver the mdr1 gene to hematopoietic stem cells in order tomake the stem cells more resistant to chemotherapy. Other referencesillustrating the use of retroviral vectors in gene therapy are: Cloweset al., J. Clin. Invest. 93:644-651 (1994); Kiem et al., Blood83:1467-1473 (1994); Salmons and Gunzberg, Human Gene Therapy 4:129-141(1993); and Grossman and Wilson, Curr. Opin. in Genetics and Devel.3:110-114 (1993). Lentiviral vectors contemplated for use include, forexample, the HIV based vectors described in U.S. Pat. Nos. 6,143,520;5,665,557; and 5,981,276, which are herein incorporated by reference.

Adenoviruses are also contemplated for use in delivery of iRNAs of theinvention. Adenoviruses are especially attractive vehicles, e.g., fordelivering genes to respiratory epithelia. Adenoviruses naturally infectrespiratory epithelia where they cause a mild disease. Other targets foradenovirus-based delivery systems are liver, the central nervous system,endothelial cells, and muscle. Adenoviruses have the advantage of beingcapable of infecting non-dividing cells. Kozarsky and Wilson, CurrentOpinion in Genetics and Development 3:499-503 (1993) present a review ofadenovirus-based gene therapy. Bout et al., Human Gene Therapy 5:3-10(1994) demonstrated the use of adenovirus vectors to transfer genes tothe respiratory epithelia of rhesus monkeys. Other instances of the useof adenoviruses in gene therapy can be found in Rosenfeld et al.,Science 252:431-434 (1991); Rosenfeld et al., Cell 68:143-155 (1992);Mastrangeli et al., J. Clin. Invest. 91:225-234 (1993); PCT PublicationWO94/12649; and Wang, et al., Gene Therapy 2:775-783 (1995). A suitableAV vector for expressing an iRNA featured in the invention, a method forconstructing the recombinant AV vector, and a method for delivering thevector into target cells, are described in Xia H et al. (2002), Nat.Biotech. 20: 1006-1010.

Adeno-associated virus (AAV) vectors may also be used to delivery aniRNA of the invention (Walsh et al., Proc. Soc. Exp. Biol. Med.204:289-300 (1993); U.S. Pat. No. 5,436,146). In one embodiment, theiRNA can be expressed as two separate, complementary single-stranded RNAmolecules from a recombinant AAV vector having, for example, either theU6 or H1 RNA promoters, or the cytomegalovirus (CMV) promoter. SuitableAAV vectors for expressing the dsRNA featured in the invention, methodsfor constructing the recombinant AV vector, and methods for deliveringthe vectors into target cells are described in Samulski R et al. (1987),J. Virol. 61: 3096-3101; Fisher K J et al. (1996), J. Virol, 70:520-532; Samulski R et al. (1989), J. Virol. 63: 3822-3826; U.S. Pat.Nos. 5,252,479; 5,139,941; International Patent Application No. WO94/13788; and International Patent Application No. WO 93/24641, theentire disclosures of which are herein incorporated by reference.

Another viral vector sui for delivery of an iRNA of the invention is apox virus such as a vaccinia virus, for example an attenuated vacciniasuch as Modified Virus Ankara (MVA) or NYVAC, an avipox such as fowl poxor canary pox.

The tropism of viral vectors can be modified by pseudotyping the vectorswith envelope proteins or other surface antigens from other viruses, orby substituting different viral capsid proteins, as appropriate. Forexample, lentiviral vectors can be pseudotyped with surface proteinsfrom vesicular stomatitis virus (VSV), rabies, Ebola, Mokola, and thelike. AAV vectors can be made to target different cells by engineeringthe vectors to express different capsid protein serotypes; see, e.g.,Rabinowitz J E et al. (2002), J Virol 76:791-801, the entire disclosureof which is herein incorporated by reference.

The pharmaceutical preparation of a vector can include the vector in anacceptable diluent, or can include a slow release matrix in which thegene delivery vehicle is imbedded. Alternatively, where the completegene delivery vector can be produced intact from recombinant cells,e.g., retroviral vectors, the pharmaceutical preparation can include oneor more cells which produce the gene delivery system.

V. Pharmaceutical Compositions of the Invention

The present invention also includes pharmaceutical compositions andformulations which include the iRNAs of the invention. In oneembodiment, provided herein are pharmaceutical compositions containingan iRNA, as described herein, and a pharmaceutically acceptable carrier.

The phrase “pharmaceutically acceptable” is employed herein to refer tothose compounds, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human subjects and animal subjects without excessivetoxicity, irritation, allergic response, or other problem orcomplication, commensurate with a reasonable benefit/risk ratio.

The phrase “pharmaceutically-acceptable carrier” as used herein means apharmaceutically-acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, manufacturing aid (e.g.,lubricant, talc magnesium, calcium or zinc stearate, or steric acid), orsolvent encapsulating material, involved in carrying or transporting thesubject compound from one organ, or portion of the body, to anotherorgan, or portion of the body. Each carrier must be “acceptable” in thesense of being compatible with the other ingredients of the formulationand not injurious to the subject being treated. Some examples ofmaterials which can serve as pharmaceutically-acceptable carriersinclude: (1) sugars, such as lactose, glucose and sucrose; (2) starches,such as corn starch and potato starch; (3) cellulose, and itsderivatives, such as sodium carboxymethyl cellulose, ethyl cellulose andcellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7)lubricating agents, such as magnesium state, sodium lauryl sulfate andtalc; (8) excipients, such as cocoa butter and suppository waxes; (9)oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil,olive oil, corn oil and soybean oil; (10) glycols, such as propyleneglycol; (11) polyols, such as glycerin, sorbitol, mannitol andpolyethylene glycol; (12) esters, such as ethyl oleate and ethyllaurate; (13) agar; (14) buffering agents, such as magnesium hydroxideand aluminum hydroxide; (15) alginic acid; (16) pyrogen-free water; (17)isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pHbuffered solutions; (21) polyesters, polycarbonates and/orpolyanhydrides; (22) bulking agents, such as polypeptides and aminoacids (23) serum component, such as serum albumin, HDL and LDL; and (22)other non-toxic compatible substances employed in pharmaceuticalformulations.

The pharmaceutical compositions containing the iRNA are useful fortreating a disease or disorder associated with the expression oractivity of a PCSK9, e.g. a disease or disorder that would benefit fromreduction in PCSK9 expression. Such pharmaceutical compositions areformulated based on the mode of delivery. One example is compositionsthat are formulated for systemic administration via parenteral delivery,e.g., by subcutaneous (SC), intramuscular (IM), or intravenous (IV)delivery. Another example is compositions that are formulated for directdelivery into the brain parenchyma, e.g., by infusion into the brain,such as by continuous pump infusion. The pharmaceutical compositions ofthe invention may be administered in dosages sufficient to inhibitexpression of a PCSK9 gene.

Preferably, in the methods of the invention an iRNA agent isadministered to a subject as a fixed dose. In one particular embodiment,a fixed dose of an iRNA agent of the invention is based on apredetermined weight or age.

In some embodiments, the RNAi agent is administered as a fixed dose ofbetween about 200 mg to about 850 mg, between about 200 mg to about 500mg, between about 200 mg to about 400 mg, between about 200 mg to about300 mg, between about 100 mg to about 800 mg, between about 100 mg toabout 750 mg, between about 100 mg to about 700 mg, between about 100 mgto about 650 mg, between about 100 mg to about 600 mg, between about 100mg to about 550 mg, between about 100 mg to about 500 mg, between about200 mg to about 850 mg, between about 200 mg to about 800 mg, betweenabout 200 mg to about 750 mg, between about 200 mg to about 700 mg,between about 200 mg to about 650 mg, between about 200 mg to about 600mg, between about 200 mg to about 550 mg, between about 200 mg to about500 mg, between about 300 mg to about 850 mg, between about 300 mg toabout 800 mg, between about 300 mg to about 750 mg, between about 300 mgto about 700 mg, between about 300 mg to about 650 mg, between about 300mg to about 600 mg, between about 300 mg to about 550 mg, between about300 mg to about 500 mg, between about 400 mg to about 850 mg, betweenabout 400 mg to about 800 mg, between about 400 mg to about 750 mg,between about 400 mg to about 700 mg, between about 400 mg to about 650mg, between about 400 mg to about 600 mg, between about 400 mg to about550 mg, or between about 400 mg to about 500 mg.

In some embodiments, the RNAi agent is administered as a fixed dose ofabout 100 mg, about 125 mg, about 150 mg, about 175 mg, 200 mg, about225 mg, about 250 mg, about 275 mg, about 300 mg, about 325 mg, about350 mg, about 375 mg, about 400 mg, about 425 mg, about 450 mg, about475 mg, about 500 mg, about 525 mg, about 550 mg, about 575 mg, about600 mg, about 625 mg, about 650 mg, about 675 mg, about 700 mg, about725 mg, about 750 mg, about 775 mg, about 800 mg, about 825 mg, or about850 mg.

In some embodiments, subjects are administered, e.g., subcutaneously orintramuscularly, multiple doses of a therapeutic amount of iRNA.

The iRNA may be formulated in a pharmaceutical composition at a suitableconcentration such that a suitable volume of the composition isadministered to the subject, such as about 1.0 mls, 1.1 mls, 1.2 mls,1.3 mls, 1.4 mls, 1.5 mls, 1.6 mls, 1.7 mls, 1.8 mls, 1.9 mls, or about2.0 mls of a pharmaceutical composition. For example, in one embodiment,an iRNA agent of the invention is formulated in a suitablepharmaceutical formulation at about 200 mg/ml such that administrationof about 1.5 mls of the formulation to a subject provides a 300 mg fixeddose of the agent.

As described herein, a single dose of the iRNA agents or pharmaceuticalcompositions comprising such agents can be long lasting, such thatsubsequent doses are administered at not more than 1 week, 2 weeks, 1month, 2 month, 3 month, 4 month, 5 month, or 6 month intervals.

In some embodiments, subjects are administered, e.g., subcutaneously orintramuscularly, a repeat dose of a therapeutic amount of iRNA. Arepeat-dose regimen may include administration of a therapeutic amountof iRNA on a regular basis, such as once a month, once every two months,once a quarter, once every four months, once every five months, orbiannually. In some embodiments of the invention, a single dose of thepharmaceutical compositions of the invention is administered once perquarter (qQ). In other embodiments of the invention, a single dose ofthe pharmaceutical compositions of the invention is administeredbi-annually (i.e., every six months). Administration can be repeated,e.g., once every quarter for 6 months, one year, two years or longer,e.g., administered chronically.

In some embodiments, the RNAi agent is administered in a dosing regimenthat includes a loading phase followed by a maintenance phase.

The loading phase may include a single administration of the RNAi agentduring the first week, a single administration of the RNAi agent duringthe first two weeks, or a single administration of the RNAi agent duringthe first month at a fixed dose of, for example, about 100 mg to about700 mg, about 150 mg to about 700 mg, about 200 mg to about 700 mg,about 250 mg to about 700 mg, about 300 mg to about 700 mg, about 350 mgto about 700 mg, about 400 mg to about 700 mg, about 450 mg to about 700mg, about 500 mg to about 700 mg, about 550 mg to about 700 mg, about600 to about 700 mg, about 650 to about 700 mg, about 100 mg to about650 mg, about 150 mg to about 650 mg, about 200 mg to about 650 mg,about 250 mg to about 650 mg, about 300 mg to about 650 mg, about 350 mgto about 650 mg, about 400 mg to about 650 mg, about 450 mg to about 650mg, about 500 mg to about 650 mg, about 550 mg to about 650 mg, about600 to about 650 mg, about 100 mg to about 600 mg, about 150 mg to about600 mg, about 200 mg to about 600 mg, about 250 mg to about 600 mg,about 300 mg to about 600 mg, about 350 mg to about 600 mg, about 400 mgto about 600 mg, about 450 mg to about 600 mg, about 500 mg to about 600mg, about 550 mg to about 600 mg, about 100 mg to about 550 mg, about150 mg to about 550 mg, about 200 mg to about 550 mg, about 250 mg toabout 550 mg, about 300 mg to about 550 mg, about 350 mg to about 550mg, about 400 mg to about 550 mg, about 450 mg to about 550 mg, about500 mg to about 550 mg, about 100 mg to about 500 mg, about 150 mg toabout 500 mg, about 200 mg to about 500 mg, about 250 mg to about 500mg, about 300 mg to about 500 mg, about 350 mg to about 500 mg, about400 mg to about 500 mg, or about 450 mg to about 500 mg, e.g., a fixeddose of about 100 mg, about 125 mg, about 150 mg, about 175 mg, 200 mg,about 225 mg, about 250 mg, about 275 mg, about 300 mg, about 325 mg,about 350 mg, about 375 mg, about 400 mg, about 425 mg, about 450 mg,about 475 mg, about 500 mg, about 525 mg, about 550 mg, about 575 mg,about 600 mg, about 625 mg, about 650 mg, about 675 mg, or about 700 mg.Values and ranges intermediate to the foregoing recited values are alsointended to be part of this invention.

The maintenance phase may include administration of a dose of the RNAiagent to the subject once a month, once every two months, once everythree months, once every four months, once every five months, or onceevery six months. In one particular embodiment, the maintenance dose isadministered to the subject once a month.

The maintenance dose or doses can be the same or lower than the initialdose, e.g., one-half of the initial dose. For example, a maintenancedose may be about 25 mg to about 100 mg administered to the subjectmonthly, for example about 25 mg to about 75 mg, about 25 mg to about 50mg, or about 50 mg to about 75 mg, e.g., about 25 mg, about 30 mg, about35 mg, about 40 mg, about 45 mg, about 50 mg, about 55 mg, about 60 mg,about 65 mg, about 70 mg, about 75 mg, about 80 mg, about 85 mg, about90 mg, about 95 mg, or about 100 mg. Values and ranges intermediate tothe foregoing recited values are also intended to be part of thisinvention.

The pharmaceutical composition can be administered by intravenousinfusion over a period of time, such as over a 5, 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, and 21, 22, 23, 24, or about a 25minute period. The administration may be repeated, for example, on aregular basis, such as weekly, biweekly (i.e., every two weeks) for onemonth, two months, three months, four months or longer. After an initialtreatment regimen, the treatments can be administered on a less frequentbasis. For example, after administration weekly or biweekly for threemonths, administration can be repeated once per month, for six months ora year or longer.

The skilled artisan will appreciate that certain factors can influencethe dosage and timing required to effectively treat a subject, includingbut not limited to the severity of the disease or disorder, previoustreatments, the general health and/or age of the subject, and otherdiseases present. Moreover, treatment of a subject with atherapeutically effective amount of a composition can include a singletreatment or a series of treatments. Estimates of effective dosages andin vivo half-lives for the individual iRNAs encompassed by the inventioncan be made using conventional methodologies or on the basis of in vivotesting using an appropriate animal model, as described elsewhereherein.

The pharmaceutical compositions of the present invention can beadministered in a number of ways depending upon whether local orsystemic treatment is desired and upon the area to be treated.Administration can be topical (e.g., by a transdermal patch), pulmonary,e.g., by inhalation or insufflation of powders or aerosols, including bynebulizer; intratracheal, intranasal, epidermal and transdermal, oral orparenteral. Parenteral administration includes intravenous,intraarterial, subcutaneous, intraperitoneal or intramuscular injectionor infusion; subdermal, e.g., via an implanted device; or intracranial,e.g., by intraparenchymal, intrathecal or intraventricular,administration.

The iRNA can be delivered in a manner to target a particular tissue,such as the liver (e.g., the hepatocytes of the liver).

Pharmaceutical compositions and formulations for topical administrationcan include transdermal patches, ointments, lotions, creams, gels,drops, suppositories, sprays, liquids and powders. Conventionalpharmaceutical carriers, aqueous, powder or oily bases, thickeners andthe like can be necessary or desirable. Coated condoms, gloves and thelike can also be useful. Suitable topical formulations include those inwhich the iRNAs featured in the invention are in admixture with atopical delivery agent such as lipids, liposomes, fatty acids, fattyacid esters, steroids, chelating agents and surfactants. Suitable lipidsand liposomes include neutral (e.g., dioleoylphosphatidyl DOPEethanolamine, dimyristoylphosphatidyl choline DMPC,distearolyphosphatidyl choline) negative (e.g., dimyristoylphosphatidylglycerol DMPG) and cationic (e.g., dioleoyltetramethylaminopropyl DOTAPand dioleoylphosphatidyl ethanolamine DOTMA). iRNAs featured in theinvention can be encapsulated within liposomes or can form complexesthereto, in particular to cationic liposomes. Alternatively, iRNAs canbe complexed to lipids, in particular to cationic lipids. Suitable fattyacids and esters include but are not limited to arachidonic acid, oleicacid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristicacid, palmitic acid, stearic acid, linoleic acid, linolenic acid,dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate,1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or aC₁₋₂₀ alkyl ester (e.g., isopropylmyristate IPM), monoglyceride,diglyceride or pharmaceutically acceptable salt thereof). Topicalformulations are described in detail in U.S. Pat. No. 6,747,014, whichis incorporated herein by reference.

Compositions and formulations for oral administration include powders orgranules, microparticulates, nanoparticulates, suspensions or solutionsin water or non-aqueous media, capsules, gel capsules, sachets, tabletsor minitablets. Thickeners, flavoring agents, diluents, emulsifiers,dispersing aids or binders can be desirable. In some embodiments, oralformulations are those in which dsRNAs featured in the invention areadministered in conjunction with one or more penetration enhancersurfactants and chelators. Suitable surfactants include fatty acidsand/or esters or salts thereof, bile acids and/or salts thereof.Suitable bile acids/salts include chenodeoxycholic acid (CDCA) andursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid,deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid,taurocholic acid, taurodeoxycholic acid, sodiumtauro-24,25-dihydro-fusidate and sodium glycodihydrofusidate. Suitablefatty acids include arachidonic acid, undecanoic acid, oleic acid,lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid,stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate,monoolein, dilaurin, glyceryl 1-monocaprate,1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or amonoglyceride, a diglyceride or a pharmaceutically acceptable saltthereof (e.g., sodium). In some embodiments, combinations of penetrationenhancers are used, for example, fatty acids/salts in combination withbile acids/salts. One exemplary combination is the sodium salt of lauricacid, capric acid and UDCA. Further penetration enhancers includepolyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. DsRNAsfeatured in the invention can be delivered orally, in granular formincluding sprayed dried particles, or complexed to form micro ornanoparticles. DsRNA complexing agents include poly-amino acids;polyimines; polyacrylates; polyalkylacrylates, polyoxethanes,polyalkylcyanoacrylates; cationized gelatins, albumins, starches,acrylates, polyethyleneglycols (PEG) and starches;polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans,celluloses and starches. Suitable complexing agents include chitosan,N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine,polyspermines, protamine, polyvinylpyridine,polythiodiethylaminomethylethylene P(TDAE), polyaminostyrene (e.g.,p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate),poly(butylcyanoacrylate), poly(isobutylcyanoacrylate),poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate,DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate,polyhexylacrylate, poly(D,L-lactic acid), poly(DL-lactic-co-glycolicacid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulationsfor dsRNAs and their preparation are described in detail in U.S. Pat.No. 6,887,906, US Publn. No. 20030027780, and U.S. Pat. No. 6,747,014,each of which is incorporated herein by reference.

Compositions and formulations for parenteral, intraparenchymal (into thebrain), intrathecal, intraventricular or intrahepatic administration caninclude sterile aqueous solutions which can also contain buffers,diluents and other suitable additives such as, but not limited to,penetration enhancers, carrier compounds and other pharmaceuticallyacceptable carriers or excipients.

Pharmaceutical compositions of the present invention include, but arenot limited to, solutions, emulsions, and liposome-containingformulations. These compositions can be generated from a variety ofcomponents that include, but are not limited to, preformed liquids,self-emulsifying solids and self-emulsifying semisolids. Particularlypreferred are formulations that target the liver when treating hepaticdisorders such as hepatic carcinoma.

The pharmaceutical formulations of the present invention, which canconveniently be presented in unit dosage form, can be prepared accordingto conventional techniques well known in the pharmaceutical industry.Such techniques include the step of bringing into association the activeingredients with the pharmaceutical carrier(s) or excipient(s). Ingeneral, the formulations are prepared by uniformly and intimatelybringing into association the active ingredients with liquid carriers orfinely divided solid carriers or both, and then, if necessary, shapingthe product.

The compositions of the present invention can be formulated into any ofmany possible dosage forms such as, but not limited to, tablets,capsules, gel capsules, liquid syrups, soft gels, suppositories, andenemas. The compositions of the present invention can also be formulatedas suspensions in aqueous, non-aqueous or mixed media. Aqueoussuspensions can further contain substances which increase the viscosityof the suspension including, for example, sodium carboxymethylcellulose,sorbitol and/or dextran. The suspension can also contain stabilizers.

A. Additional Formulations

i. Emulsions

The compositions of the present invention can be prepared and formulatedas emulsions. Emulsions are typically heterogeneous systems of oneliquid dispersed in another in the form of droplets usually exceeding0.1 μm in diameter (see e.g., Ansel's Pharmaceutical Dosage Forms andDrug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004,Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Idson, inPharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988,Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, inPharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988,Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block inPharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988,Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al.,in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton,Pa., 1985, p. 301). Emulsions are often biphasic systems comprising twoimmiscible liquid phases intimately mixed and dispersed with each other.In general, emulsions can be of either the water-in-oil (w/o) or theoil-in-water (o/w) variety. When an aqueous phase is finely divided intoand dispersed as minute droplets into a bulk oily phase, the resultingcomposition is called a water-in-oil (w/o) emulsion. Alternatively, whenan oily phase is finely divided into and dispersed as minute dropletsinto a bulk aqueous phase, the resulting composition is called anoil-in-water (o/w) emulsion. Emulsions can contain additional componentsin addition to the dispersed phases, and the active drug which can bepresent as a solution in either the aqueous phase, oily phase or itselfas a separate phase. Pharmaceutical excipients such as emulsifiers,stabilizers, dyes, and anti-oxidants can also be present in emulsions asneeded. Pharmaceutical emulsions can also be multiple emulsions that arecomprised of more than two phases such as, for example, in the case ofoil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions.Such complex formulations often provide certain advantages that simplebinary emulsions do not. Multiple emulsions in which individual oildroplets of an o/w emulsion enclose small water droplets constitute aw/o/w emulsion. Likewise a system of oil droplets enclosed in globulesof water stabilized in an oily continuous phase provides an o/w/oemulsion.

Emulsions are characterized by little or no thermodynamic stability.Often, the dispersed or discontinuous phase of the emulsion is welldispersed into the external or continuous phase and maintained in thisform through the means of emulsifiers or the viscosity of theformulation. Either of the phases of the emulsion can be a semisolid ora solid, as is the case of emulsion-style ointment bases and creams.Other means of stabilizing emulsions entail the use of emulsifiers thatcan be incorporated into either phase of the emulsion. Emulsifiers canbroadly be classified into four categories: synthetic surfactants,naturally occurring emulsifiers, absorption bases, and finely dispersedsolids (see e.g., Ansel's Pharmaceutical Dosage Forms and Drug DeliverySystems, Allen, L V., Popovich N G., and Ansel H C., 2004, LippincottWilliams & Wilkins (8th ed.), New York, N.Y.; Idson, in PharmaceuticalDosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker,Inc., New York, N.Y., volume 1, p. 199).

Synthetic surfactants, also known as surface active agents, have foundwide applicability in the formulation of emulsions and have beenreviewed in the literature (see e.g., Ansel's Pharmaceutical DosageForms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel HC., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.;Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285;Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker(Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199).Surfactants are typically amphiphilic and comprise a hydrophilic and ahydrophobic portion. The ratio of the hydrophilic to the hydrophobicnature of the surfactant has been termed the hydrophile/lipophilebalance (HLB) and is a valuable tool in categorizing and selectingsurfactants in the preparation of formulations. Surfactants can beclassified into different classes based on the nature of the hydrophilicgroup: nonionic, anionic, cationic and amphoteric (see e.g., Ansel'sPharmaceutical Dosage Forms and Drug Delivery Systems, Allen, L V.,Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins (8thed.), New York, N.Y. Rieger, in Pharmaceutical Dosage Forms, Lieberman,Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y.,volume 1, p. 285).

Naturally occurring emulsifiers used in emulsion formulations includelanolin, beeswax, phosphatides, lecithin and acacia. Absorption basespossess hydrophilic properties such that they can soak up water to formw/o emulsions yet retain their semisolid consistencies, such asanhydrous lanolin and hydrophilic petrolatum. Finely divided solids havealso been used as good emulsifiers especially in combination withsurfactants and in viscous preparations. These include polar inorganicsolids, such as heavy metal hydroxides, nonswelling clays such asbentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidalaluminum silicate and colloidal magnesium aluminum silicate, pigmentsand nonpolar solids such as carbon or glyceryl tristearate.

A large variety of non-emulsifying materials are also included inemulsion formulations and contribute to the properties of emulsions.These include fats, oils, waxes, fatty acids, fatty alcohols, fattyesters, humectants, hydrophilic colloids, preservatives and antioxidants(Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335;Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

Hydrophilic colloids or hydrocolloids include naturally occurring gumsand synthetic polymers such as polysaccharides (for example, acacia,agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth),cellulose derivatives (for example, carboxymethylcellulose andcarboxypropylcellulose), and synthetic polymers (for example, carbomers,cellulose ethers, and carboxyvinyl polymers). These disperse or swell inwater to form colloidal solutions that stabilize emulsions by formingstrong interfacial films around the dispersed-phase droplets and byincreasing the viscosity of the external phase.

Since emulsions often contain a number of ingredients such ascarbohydrates, proteins, sterols and phosphatides that can readilysupport the growth of microbes, these formulations often incorporatepreservatives. Commonly used preservatives included in emulsionformulations include methyl paraben, propyl paraben, quaternary ammoniumsalts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boricacid. Antioxidants are also commonly added to emulsion formulations toprevent deterioration of the formulation. Antioxidants used can be freeradical scavengers such as tocopherols, alkyl gallates, butylatedhydroxyanisole, butylated hydroxytoluene, or reducing agents such asascorbic acid and sodium metabisulfite, and antioxidant synergists suchas citric acid, tartaric acid, and lecithin.

The application of emulsion formulations via dermatological, oral andparenteral routes and methods for their manufacture have been reviewedin the literature (see e.g., Ansel's Pharmaceutical Dosage Forms andDrug Delivery Systems, Allen, L V., Popovich N G., and Ansel H C., 2004,Lippincott Williams & Wilkins (8th ed.), New York, N.Y.; Idson, inPharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988,Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsionformulations for oral delivery have been very widely used because ofease of formulation, as well as efficacy from an absorption andbioavailability standpoint (see e.g., Ansel's Pharmaceutical DosageForms and Drug Delivery Systems, Allen, L V., Popovich N G., and Ansel HC., 2004, Lippincott Williams & Wilkins (8th ed.), New York, N.Y.;Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245;Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker(Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritivepreparations are among the materials that have commonly beenadministered orally as o/w emulsions.

ii. Microemulsions

In one embodiment of the present invention, the compositions of iRNAsand nucleic acids are formulated as microemulsions. A microemulsion canbe defined as a system of water, oil and amphiphile which is a singleoptically isotropic and thermodynamically stable liquid solution (seee.g., Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems,Allen, L V., Popovich N G., and Ansel H C., 2004, Lippincott Williams &Wilkins (8th ed.), New York, N.Y.; Rosoff, in Pharmaceutical DosageForms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc.,New York, N.Y., volume 1, p. 245). Typically microemulsions are systemsthat are prepared by first dispersing an oil in an aqueous surfactantsolution and then adding a sufficient amount of a fourth component,generally an intermediate chain-length alcohol to form a transparentsystem. Therefore, microemulsions have also been described asthermodynamically stable, isotropically clear dispersions of twoimmiscible liquids that are stabilized by interfacial films ofsurface-active molecules (Leung and Shah, in: Controlled Release ofDrugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCHPublishers, New York, pages 185-215). Microemulsions commonly areprepared via a combination of three to five components that include oil,water, surfactant, cosurfactant and electrolyte. Whether themicroemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) typeis dependent on the properties of the oil and surfactant used and on thestructure and geometric packing of the polar heads and hydrocarbon tailsof the surfactant molecules (Schott, in Remington's PharmaceuticalSciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).

The phenomenological approach utilizing phase diagrams has beenextensively studied and has yielded a comprehensive knowledge, to oneskilled in the art, of how to formulate microemulsions (see e.g.,Ansel's Pharmaceutical Dosage Forms and Drug Delivery Systems, Allen, LV., Popovich N G., and Ansel H C., 2004, Lippincott Williams & Wilkins(8th ed.), New York, N.Y.; Rosoff, in Pharmaceutical Dosage Forms,Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., NewYork, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms,Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., NewYork, N.Y., volume 1, p. 335). Compared to conventional emulsions,microemulsions offer the advantage of solubilizing water-insoluble drugsin a formulation of thermodynamically stable droplets that are formedspontaneously.

Surfactants used in the preparation of microemulsions include, but arenot limited to, ionic surfactants, non-ionic surfactants, Brij 96,polyoxyethylene oleyl ethers, polyglycerol fatty acid esters,tetraglycerol monolaurate (ML310), tetraglycerol monooleate (M0310),hexaglycerol monooleate (P0310), hexaglycerol pentaoleate (P0500),decaglycerol monocaprate (MCA750), decaglycerol monooleate (M0750),decaglycerol sequioleate (S0750), decaglycerol decaoleate (DA0750),alone or in combination with cosurfactants. The cosurfactant, usually ashort-chain alcohol such as ethanol, 1-propanol, and 1-butanol, servesto increase the interfacial fluidity by penetrating into the surfactantfilm and consequently creating a disordered film because of the voidspace generated among surfactant molecules. Microemulsions can, however,be prepared without the use of cosurfactants and alcohol-freeself-emulsifying microemulsion systems are known in the art. The aqueousphase can typically be, but is not limited to, water, an aqueoussolution of the drug, glycerol, PEG300, PEG400, polyglycerols, propyleneglycols, and derivatives of ethylene glycol. The oil phase can include,but is not limited to, materials such as Captex 300, Captex 355, CapmulMCM, fatty acid esters, medium chain (C8-C12) mono, di, andtri-glycerides, polyoxyethylated glyceryl fatty acid esters, fattyalcohols, polyglycolized glycerides, saturated polyglycolized C8-C10glycerides, vegetable oils and silicone oil.

Microemulsions are particularly of interest from the standpoint of drugsolubilization and the enhanced absorption of drugs. Lipid basedmicroemulsions (both o/w and w/o) have been proposed to enhance the oralbioavailability of drugs, including peptides (see e.g., U.S. Pat. Nos.6,191,105; 7,063,860; 7,070,802; 7,157,099; Constantinides et al.,Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp.Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages ofimproved drug solubilization, protection of drug from enzymatichydrolysis, possible enhancement of drug absorption due tosurfactant-induced alterations in membrane fluidity and permeability,ease of preparation, ease of oral administration over solid dosageforms, improved clinical potency, and decreased toxicity (see e.g., U.S.Pat. Nos. 6,191,105; 7,063,860; 7,070,802; 7,157,099; Constantinides etal., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci.,1996, 85, 138-143). Often microemulsions can form spontaneously whentheir components are brought together at ambient temperature. This canbe particularly advantageous when formulating thermolabile drugs,peptides or iRNAs. Microemulsions have also been effective in thetransdermal delivery of active components in both cosmetic andpharmaceutical applications. It is expected that the microemulsioncompositions and formulations of the present invention will facilitatethe increased systemic absorption of iRNAs and nucleic acids from thegastrointestinal tract, as well as improve the local cellular uptake ofiRNAs and nucleic acids.

Microemulsions of the present invention can also contain additionalcomponents and additives such as sorbitan monostearate (Grill 3),Labrasol, and penetration enhancers to improve the properties of theformulation and to enhance the absorption of the iRNAs and nucleic acidsof the present invention. Penetration enhancers used in themicroemulsions of the present invention can be classified as belongingto one of five broad categories—surfactants, fatty acids, bile salts,chelating agents, and non-chelating non-surfactants (Lee et al.,Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Eachof these classes has been discussed above.

iii. Microparticles

an RNAi agent of the invention may be incorporated into a particle,e.g., a microparticle. Microparticles can be produced by spray-drying,but may also be produced by other methods including lyophilization,evaporation, fluid bed drying, vacuum drying, or a combination of thesetechniques.

iv. Penetration Enhancers

In one embodiment, the present invention employs various penetrationenhancers to effect the efficient delivery of nucleic acids,particularly iRNAs, to the skin of animals. Most drugs are present insolution in both ionized and nonionized forms. However, usually onlylipid soluble or lipophilic drugs readily cross cell membranes. It hasbeen discovered that even non-lipophilic drugs can cross cell membranesif the membrane to be crossed is treated with a penetration enhancer. Inaddition to aiding the diffusion of non-lipophilic drugs across cellmembranes, penetration enhancers also enhance the permeability oflipophilic drugs.

Penetration enhancers can be classified as belonging to one of fivebroad categories, i.e., surfactants, fatty acids, bile salts, chelatingagents, and non-chelating non-surfactants (see e.g., Malmsten, M.Surfactants and polymers in drug delivery, Informa Health Care, NewYork, N.Y., 2002; Lee et al., Critical Reviews in Therapeutic DrugCarrier Systems, 1991, p. 92). Each of the above mentioned classes ofpenetration enhancers are described below in greater detail.

Surfactants (or “surface-active agents”) are chemical entities which,when dissolved in an aqueous solution, reduce the surface tension of thesolution or the interfacial tension between the aqueous solution andanother liquid, with the result that absorption of iRNAs through themucosa is enhanced. In addition to bile salts and fatty acids, thesepenetration enhancers include, for example, sodium lauryl sulfate,polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (seee.g., Malmsten, M. Surfactants and polymers in drug delivery, InformaHealth Care, New York, N.Y., 2002; Lee et al., Critical Reviews inTherapeutic Drug Carrier Systems, 1991, p. 92); and perfluorochemicalemulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988,40, 252).

Various fatty acids and their derivatives which act as penetrationenhancers include, for example, oleic acid, lauric acid, capric acid(n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleicacid, linolenic acid, dicaprate, tricaprate, monoolein(1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid,glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acylcarnitines,acylcholines, C₁₋₂₀ alkyl esters thereof (e.g., methyl, isopropyl andt-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate,caprate, myristate, palmitate, stearate, linoleate, etc.) (see e.g.,Touitou, E., et al. Enhancement in Drug Delivery, CRC Press, Danvers,Mass., 2006; Lee et al., Critical Reviews in Therapeutic Drug CarrierSystems, 1991, p. 92; Muranishi, Critical Reviews in Therapeutic DrugCarrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol.,1992, 44, 651-654).

The physiological role of bile includes the facilitation of dispersionand absorption of lipids and fat-soluble vitamins (see e.g., Malmsten,M. Surfactants and polymers in drug delivery, Informa Health Care, NewYork, N.Y., 2002; Brunton, Chapter 38 in: Goodman & Gilman's ThePharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds.,McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts,and their synthetic derivatives, act as penetration enhancers. Thus theterm “bile salts” includes any of the naturally occurring components ofbile as well as any of their synthetic derivatives. Suitable bile saltsinclude, for example, cholic acid (or its pharmaceutically acceptablesodium salt, sodium cholate), dehydrocholic acid (sodiumdehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid(sodium glucholate), glycholic acid (sodium glycocholate),glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid(sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate),chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid(UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodiumglycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (see e.g.,Malmsten, M. Surfactants and polymers in drug delivery, Informa HealthCare, New York, N.Y., 2002; Lee et al., Critical Reviews in TherapeuticDrug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In:Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., MackPublishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, CriticalReviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto etal., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm.Sci., 1990, 79, 579-583).

Chelating agents, as used in connection with the present invention, canbe defined as compounds that remove metallic ions from solution byforming complexes therewith, with the result that absorption of iRNAsthrough the mucosa is enhanced. With regards to their use as penetrationenhancers in the present invention, chelating agents have the addedadvantage of also serving as DNase inhibitors, as most characterized DNAnucleases require a divalent metal ion for catalysis and are thusinhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618,315-339). Suitable chelating agents include but are not limited todisodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates(e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acylderivatives of collagen, laureth-9 and N-amino acyl derivatives ofbeta-diketones (enamines)(see e.g., Katdare, A. et al., Excipientdevelopment for pharmaceutical, biotechnology, and drug delivery, CRCPress, Danvers, Mass., 2006; Lee et al., Critical Reviews in TherapeuticDrug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews inTherapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. ControlRel., 1990, 14, 43-51).

As used herein, non-chelating non-surfactant penetration enhancingcompounds can be defined as compounds that demonstrate insignificantactivity as chelating agents or as surfactants but that nonethelessenhance absorption of iRNAs through the alimentary mucosa (see e.g.,Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990,7, 1-33). This class of penetration enhancers includes, for example,unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanonederivatives (Lee et al., Critical Reviews in Therapeutic Drug CarrierSystems, 1991, page 92); and non-steroidal anti-inflammatory agents suchas diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al.,J. Pharm. Pharmacol., 1987, 39, 621-626).

Agents that enhance uptake of iRNAs at the cellular level can also beadded to the pharmaceutical and other compositions of the presentinvention. For example, cationic lipids, such as lipofectin (Junichi etal, U.S. Pat. No. 5,705,188), cationic glycerol derivatives, andpolycationic molecules, such as polylysine (Lollo et al., PCTApplication WO 97/30731), are also known to enhance the cellular uptakeof dsRNAs. Examples of commercially available transfection reagentsinclude, for example Lipofectamine™ (Invitrogen; Carlsbad, Calif.),Lipofectamine 2000™ (Invitrogen; Carlsbad, Calif.), 293fectin™(Invitrogen; Carlsbad, Calif.), Cellfectin™ (Invitrogen; Carlsbad,Calif.), DMRIE-C™ (Invitrogen; Carlsbad, Calif.), FreeStyle™ MAX(Invitrogen; Carlsbad, Calif.), Lipofectamine™ 2000 CD (Invitrogen;Carlsbad, Calif.), Lipofectamine™ (Invitrogen; Carlsbad, Calif.),RNAiMAX (Invitrogen; Carlsbad, Calif.), Oligofectamine™ (Invitrogen;Carlsbad, Calif.), Optifect™ (Invitrogen; Carlsbad, Calif.), X-tremeGENEQ2 Transfection Reagent (Roche; Grenzacherstrasse, Switzerland), DOTAPLiposomal Transfection Reagent (Grenzacherstrasse, Switzerland), DOSPERLiposomal Transfection Reagent (Grenzacherstrasse, Switzerland), orFugene (Grenzacherstrasse, Switzerland), Transfectam® Reagent (Promega;Madison, Wis.), TransFast™ Transfection Reagent (Promega; Madison,Wis.), Tfx™-20 Reagent (Promega; Madison, Wis.), Tfx™-50 Reagent(Promega; Madison, Wis.), DreamFect™ (OZ Biosciences; Marseille,France), EcoTransfect (OZ Biosciences; Marseille, France), TransPassa D1Transfection Reagent (New England Biolabs; Ipswich, Mass., USA),LyoVec™/LipoGen™ (Invitrogen; San Diego, Calif., USA), PerFectinTransfection Reagent (Genlantis; San Diego, Calif., USA), NeuroPORTERTransfection Reagent (Genlantis; San Diego, Calif., USA), GenePORTERTransfection reagent (Genlantis; San Diego, Calif., USA), GenePORTER 2Transfection reagent (Genlantis; San Diego, Calif., USA), CytofectinTransfection Reagent (Genlantis; San Diego, Calif., USA), BaculoPORTERTransfection Reagent (Genlantis; San Diego, Calif., USA), TroganPORTER™transfection Reagent (Genlantis; San Diego, Calif., USA), RiboFect(Bioline; Taunton, Mass., USA), PlasFect (Bioline; Taunton, Mass., USA),UniFECTOR (B-Bridge International; Mountain View, Calif., USA),SureFECTOR (B-Bridge International; Mountain View, Calif., USA), orHiFect™ (B-Bridge International, Mountain View, Calif., USA), amongothers.

Other agents can be utilized to enhance the penetration of theadministered nucleic acids, including glycols such as ethylene glycoland propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenessuch as limonene and menthone.

v. Carriers

Certain compositions of the present invention also incorporate carriercompounds in the formulation. As used herein, “carrier compound” or“carrier” can refer to a nucleic acid, or analog thereof, which is inert(i.e., does not possess biological activity per se) but is recognized asa nucleic acid by in vivo processes that reduce the bioavailability of anucleic acid having biological activity by, for example, degrading thebiologically active nucleic acid or promoting its removal fromcirculation. The coadministration of a nucleic acid and a carriercompound, typically with an excess of the latter substance, can resultin a substantial reduction of the amount of nucleic acid recovered inthe liver, kidney or other extracirculatory reservoirs, presumably dueto competition between the carrier compound and the nucleic acid for acommon receptor. For example, the recovery of a partiallyphosphorothioate dsRNA in hepatic tissue can be reduced when it iscoadministered with polyinosinic acid, dextran sulfate, polycytidic acidor 4-acetamido-4′isothiocyano-stilbene-2,2′-disulfonic acid (Miyao etal., DsRNA Res. Dev., 1995, 5, 115-121; Takakura et al., DsRNA & Nucl.Acid Drug Dev., 1996, 6, 177-183.

vi. Excipients

In contrast to a carrier compound, a “pharmaceutical carrier” or“excipient” is a pharmaceutically acceptable solvent, suspending agentor any other pharmacologically inert vehicle for delivering one or morenucleic acids to an animal. The excipient can be liquid or solid and isselected, with the planned manner of administration in mind, so as toprovide for the desired bulk, consistency, etc., when combined with anucleic acid and the other components of a given pharmaceuticalcomposition. Typical pharmaceutical carriers include, but are notlimited to, binding agents (e.g., pregelatinized maize starch,polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers(e.g., lactose and other sugars, microcrystalline cellulose, pectin,gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calciumhydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc,silica, colloidal silicon dioxide, stearic acid, metallic stearates,hydrogenated vegetable oils, corn starch, polyethylene glycols, sodiumbenzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodiumstarch glycolate, etc.); and wetting agents (e.g., sodium laurylsulphate, etc).

Pharmaceutically acceptable organic or inorganic excipients suitable fornon-parenteral administration which do not deleteriously react withnucleic acids can also be used to formulate the compositions of thepresent invention. Suitable pharmaceutically acceptable carriersinclude, but are not limited to, water, salt solutions, alcohols,polyethylene glycols, gelatin, lactose, amylose, magnesium stearate,talc, silicic acid, viscous paraffin, hydroxymethylcellulose,polyvinylpyrrolidone and the like.

Formulations for topical administration of nucleic acids can includesterile and non-sterile aqueous solutions, non-aqueous solutions incommon solvents such as alcohols, or solutions of the nucleic acids inliquid or solid oil bases. The solutions can also contain buffers,diluents and other suitable additives. Pharmaceutically acceptableorganic or inorganic excipients suitable for non-parenteraladministration which do not deleteriously react with nucleic acids canbe used.

Suitable pharmaceutically acceptable excipients include, but are notlimited to, water, salt solutions, alcohol, polyethylene glycols,gelatin, lactose, amylose, magnesium stearate, talc, silicic acid,viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and thelike.

vii. Other Components

The compositions of the present invention can additionally contain otheradjunct components conventionally found in pharmaceutical compositions,at their art-established usage levels. Thus, for example, thecompositions can contain additional, compatible, pharmaceutically-activematerials such as, for example, antipruritics, astringents, localanesthetics or anti-inflammatory agents, or can contain additionalmaterials useful in physically formulating various dosage forms of thecompositions of the present invention, such as dyes, flavoring agents,preservatives, antioxidants, opacifiers, thickening agents andstabilizers. However, such materials, when added, should not undulyinterfere with the biological activities of the components of thecompositions of the present invention. The formulations can besterilized and, if desired, mixed with auxiliary agents, e.g.,lubricants, preservatives, stabilizers, wetting agents, emulsifiers,salts for influencing osmotic pressure, buffers, colorings, flavoringsand/or aromatic substances and the like which do not deleteriouslyinteract with the nucleic acid(s) of the formulation.

Aqueous suspensions can contain substances which increase the viscosityof the suspension including, for example, sodium carboxymethylcellulose,sorbitol and/or dextran. The suspension can also contain stabilizers.

In some embodiments, pharmaceutical compositions featured in theinvention include (a) one or more iRNA compounds and (b) one or moreagents which function by a non-RNAi mechanism and which are useful intreating a hemolytic disorder. Examples of such agents include, but arenot limited to an anti-inflammatory agent, anti-steatosis agent,anti-viral, and/or anti-fibrosis agent. In addition, other substancescommonly used to protect the liver, such as silymarin, can also be usedin conjunction with the iRNAs described herein. Other agents useful fortreating liver diseases include telbivudine, entecavir, and proteaseinhibitors such as telaprevir and other disclosed, for example, in Tunget al., U.S. Application Publication Nos. 2005/0148548, 2004/0167116,and 2003/0144217; and in Hale et al., U.S. Application Publication No.2004/0127488.

Toxicity and therapeutic efficacy of such compounds can be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., for determining the LD50 (the dose lethal to 50% of thepopulation) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dose ratio between toxic and therapeutic effects isthe therapeutic index and it can be expressed as the ratio LD50/ED50.Compounds that exhibit high therapeutic indices are preferred.

The data obtained from cell culture assays and animal studies can beused in formulating a range of dosage for use in humans. The dosage ofcompositions featured herein in the invention lies generally within arange of circulating concentrations that include the ED50 with little orno toxicity. The dosage can vary within this range depending upon thedosage form employed and the route of administration utilized. For anycompound used in the methods featured in the invention, thetherapeutically effective dose can be estimated initially from cellculture assays. A dose can be formulated in animal models to achieve acirculating plasma concentration range of the compound or, whenappropriate, of the polypeptide product of a target sequence (e.g.,achieving a decreased concentration of the polypeptide) that includesthe IC50 (i.e., the concentration of the test compound which achieves ahalf-maximal inhibition of symptoms) as determined in cell culture. Suchinformation can be used to more accurately determine useful doses inhumans. Levels in plasma can be measured, for example, by highperformance liquid chromatography.

In addition to their administration, as discussed above, the iRNAsfeatured in the invention can be administered in combination with otherknown agents effective in treatment of pathological processes mediatedby PCSK9 expression. In any event, the administering physician canadjust the amount and timing of iRNA administration on the basis ofresults observed using standard measures of efficacy known in the art ordescribed herein.

VI. Kits

The present invention also provides kits for using any of the iRNAagents and/or performing any of the methods of the invention. Such kitsinclude one or more RNAi agent(s) and instructions for use, e.g.,instructions for inhibiting expression of a PCSK9 in a cell bycontacting the cell with the RNAi agent(s) in an amount effective toinhibit expression of the PCSK9. The kits may optionally furthercomprise means for contacting the cell with the RNAi agent (e.g., aninjection device), or means for measuring the inhibition of PCSK9 (e.g.,means for measuring the inhibition of PCSK9 mRNA protein). Such meansfor measuring the inhibition of PCSK9 may comprise a means for obtaininga sample from a subject, such as, e.g., a plasma sample. The kits of theinvention may optionally further comprise means for administering theRNAi agent(s) to a subject or means for determining the therapeuticallyeffective or prophylactically effective amount.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice or testing of the iRNAs and methods featured in the invention,suitable methods and materials are described below. All publications,patent applications, patents, and other references mentioned herein, aswell as the Sequence Listing and Figures, are incorporated by referencein their entirety. In case of conflict, the present specification,including definitions, will control. In addition, the materials,methods, and examples are illustrative only and not intended to belimiting.

Examples Example 1. Synthesis of GalNAc-Conjugated Oligonucleotides

A series of siRNA duplexes targeting nucleotides 3544-3623 of the humanPCSK9 gene (SEQ ID NO:1) were designed, synthesized. These samesequences were also synthesized with various nucleotide modificationsand conjugated with a trivalent GalNAc. The sense and antisense strandsequences of the modified duplexes are shown in Table 1.

TABLE B Abbreviations of nucleotide monomers used in nucleic acidsequence representation. Abbreviation Nucleotide(s) AAdenosine-3′-phosphate Ab beta-L-adenosine-3′-phosphate Af2′-fluoroadenosine-3′-phosphate Afs2′-fluoroadenosine-3′-phosphorothioate As adenosine-3′-phosphorothioateC cytidine-3′-phosphate Cb beta-L-cytidine-3′-phosphate Cf2′-fluorocytidine-3′-phosphate Cfs 2′-fluorocytidine-3′-phosphorothioateCs cytidine-3′-phosphorothioate G guanosine-3′-phosphate Gbbeta-L-guanosine-3′-phosphate Gbs beta-L-guanosine-3′-phosphorothioateGf 2′-fluoroguanosine-3′-phosphate Gfs2′-fluoroguanosine-3′-phosphorothioate Gs guanosine-3′-phosphorothioateT 5′-methyluridine-3′-phosphate Tf2′-fluoro-5-methyluridine-3′-phosphate Tfs2′-fluoro-5-methyluridine-3′-phosphorothioate Ts5-methyluridine-3′-phosphorothioate U Uridine-3′-phosphate Uf2′-fluorouridine-3′-phosphate Ufs 2′-fluorouridine-3′-phosphorothioateUs uridine-3′-phosphorothioate N anynucleotide(G,A,C,TorU) a2′-O-methyladenosine-3′-phosphate as2′-O-methyladenosine-3′-phosphorothioate c2′-O-methylcytidine-3′-phosphate cs2′-O-methylcytidine-3′-phosphorothioate g2′-O-methylguanosine-3′-phosphate gs2′-O-methylguanosine-3′-phosphorothioate t2′-0-methyl-5-methyluridine-3′-phosphate ts2′-0-methyl-5-methyluridine-3′-phosphorothioate u2′-O-methyluridine-3′-phosphate us2′-O-methyluridine-3′-phosphorothioate dT 2′-deoxythymidine-3′-phosphatedTs 2′-deoxythymidine-3′-phosphorothioate dU2′-deoxyuridine-3′-phosphate dUs 2′-deoxyuridine-3′-phosphorothioate sphosphorothioatelinkage L96 N-[tris(GalNAc-alkyl)-amidodecanoyl)]-4-hydroxyprolinol Hyp-(GalNAc-alkyl)3 (Aeo)2′-O-methoxyethyladenosine-3′-phosphate (Aeos)2′-O-methoxyethyladenosine-3′-phosphorothioate (Geo)2′-O-methoxyethylguanosine-3′-phosphate (Geos)2′-O-methoxyethylguanosine-3′-phosphorothioate (Teo)2′-O-methoxyethyl-5-methyluridine-3′-phosphate (Teos)2′-O-methoxyethyl-5-methyluridine-3′-phosphorothioate (m5Ceo)2′-O-methoxyethyl-5-methylcytidine-3′-phosphate (m5Ceos)2′-O-methoxyethyl-5-methylcytidine-3′-phosphorothioate (A3m)3′-O-methyladenosine-2′-phosphate (A3mx)3′-O-methyl-xylofuranosyladenosine-2′-phosphate (G3m)3′-O-methylguanosine-2′-phosphate (G3mx)3′-O-methyl-xylofuranosylguanosine-2′-phosphate (C3m)3′-O-methylcytidine-2′-phosphate (C3mx)3′-O-methyl-xylofuranosylcytidine-2′-phosphate (U3m)3′-O-methyluridine-2′-phosphate (U3mx)3′-O-methylxylouridine-2′-phosphate (Chd)2′-O-hexadecyl-cytidine-3′-phosphate (pshe) Hydroxyethylphosphorothioate(Uhd) 2′-O-hexadecyl-uridine-3′-phosphate (Tgn)Thymidine-glycolnucleicacid(GNA)S-Isomer (Cgn)Cytidine-glycolnucleicacid(GNA) (Chd)2′-O-hexadecyl-cytidine-3′-phosphate (Ggn)2′-O-hexadecyl-cytidine-3′-phosphate (Agn)Adenosine-glycolnucleicacid(GNA) P 5′-phosphate (m5Cam)2′-O-(N-methylacetamide)-5-methylcytidine-3′-phosphate (m5Cams)2′-O-(N-methylacetamide)-5-methylcytidine- 3′-phosphorothioate (Tam)2′-O-(N-methylacetamide)thymidine-3′-phosphate (Tams)2′-O-(N-methylacetamide)thymidine-3′-phosphorothioate (Aam)2′-O-(N-methylacetamide)adenosine-3′-phosphate (Aams)2′-O-(N-methylacetamide)adenosine-3′-phosphorothioate (Gam)2′-O-(N-methylacetamide)guanosine-3′-phosphate (Gams)2′-O-(N-methylacetamide)guanosine-3′-phosphorothioate (Uyh)2′-O-(1-hexyl-4-methylene-l,2,3-triazolyl)- uridine-3′-phosphate (Ayh)2′-O-(1-hexyl-4-methylene-l,2,3-triazolyl)- adenosine-3′-phosphate (Gyh)2′-O-(1-hexyl-4-methylene-l,2,3-triazolyl)- guanosine-3′-phosphate (Cyh)2′-O-(1-hexyl-4-methylene-l,2,3-triazolyl)- cytidine-3′-phosphate (iA)invertedadenosine-5′-phosphate (iC) invertedcytidine-5′-phosphate

TABLE 1Double-Stranded Ribonucleic Acid (RNAi) Agents Targeting Nucleotides 3544-3623 of Human  PCSK9 (SEQ ID NO: 1). SEQ Sense Start SEQ Antisense Duplex Sense IDSequence In NM_174 Antisense ID Sequence ID ID NO: (5′ to 3′) 936.3 IDNO: (5′ to 3′) AD-53806 A-110717 7 CfaAfgCfaGfaCfAfUf 3544 A-109589 8aAfaAfaGfaUfaAfaug uUfaUfcUfuUfuUfL96 UfellfgCfuUfgsCfsu AD-53806A-110717 9 CfaAfgCfaGfaCfAfUf 3544 A-109589 10 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-53806 A-110717 11CfaAfgCfaGfaCfAfUf 3544 A-109589 12 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-53806 A-110717 13CfaAfgCfaGfaCfAfUf 3544 A-109589 14 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-53806 A-110717 15CfaAfgCfaGfaCfAfUf 3544 A-109589 16 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-53806 A-110717 17CfaAfgCfaGfaCfAfUf 3544 A-109589 18 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-53806 A- 19 CfaAfgCfaGfaCfAfUf3544 A-109589 20 aAfaAfaGfaUfaAfaug 110717.6 uUfaUfcUfuUfuUfL96UfcUfgCfuUfgsCfsu AD-53806 A- 21 CfaAfgCfaGfaCfAfUf 3544 A-109589 22aAfaAfaGfaUfaAfaug 110717.7 uUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsuAD-53806 A- 23 CfaAfgCfaGfaCfAfUf 3544 A-109589 24 aAfaAfaGfaUfaAfaug110717.8 uUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-53806 A- 25CfaAfgCfaGfaCfAfUf 3544 A-109589 26 aAfaAfaGfaUfaAfaug 110717.9uUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56979 A-116393 27caAfgCfaGfaCfAfUfu 3544 A-109589 28 aAfaAfaGfaUfaAfaug UfaUfcUfuUfuUfL96UfcUfgCfuUfgsCfsu AD-56979 A-116393 29 caAfgCfaGfaCfAfUfu 3544 A-10958930 aAfaAfaGfaUfaAfaug UfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56975A-116394 31 (iC)aAfgCfaGfaCfAf 3544 A-109589 32 aAfaAfaGfaUfaAfaugUfuUfaUfcUfuUfuUfL UfcUfgCfuUfgsCfsu 96 AD-56975 A-116394 33(iC)aAfgCfaGfaCfAf 3544 A-109589 34 aAfaAfaGfaUfaAfaugUfuUfaUfcUfuUfuUfL UfcUfgCfuUfgsCfsu 96 AD-56975 A-116394 35(iC)aAfgCfaGfaCfAf 3544 A-109589 36 aAfaAfaGfaUfaAfaugUfuUfaUfcUfuUfuUfL UfcUfgCfuUfgsCfsu 96 AD-56975 A-116394 37(iC)aAfgCfaGfaCfAf 3544 A-109589 38 aAfaAfaGfaUfaAfaugUfuUfaUfcUfuUfuUfL UfcUfgCfuUfgsCfsu 96 AD-56975 A-116394 39(iC)aAfgCfaGfaCfAf 3544 A-109589 40 aAfaAfaGfaUfaAfaugUfuUfaUfcUfuUfuUfL UfcUfgCfuUfgsCfsu 96 AD-56983 A-116400 41CbaAfgCfaGfaCfAfUf 3544 A-109589 42 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56983 A-116400 43CbaAfgCfaGfaCfAfUf 3544 A-109589 44 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56983 A-116400 45CbaAfgCfaGfaCfAfUf 3544 A-109589 46 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56983 A-116400 47CbaAfgCfaGfaCfAfUf 3544 A-109589 48 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56983 A-116400 49CbaAfgCfaGfaCfAfUf 3544 A-109589 50 aAfaAfaGfaUfaAfauguUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56977 A-116406 51CfaagCfaGfaCfAfUfu 3544 A-109589 52 aAfaAfaGfaUfaAfaug UfaUfcUfuUfuUfL96UfcUfgCfuUfgsCfsu AD-56977 A-116406 53 CfaagCfaGfaCfAfUfu 3544 A-10958954 aAfaAfaGfaUfaAfaug UfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56977A-116406 55 CfaagCfaGfaCfAfUfu 3544 A-109589 56 aAfaAfaGfaUfaAfaugUfaUfcUfuUfuUfL96 UfcUfgCfuUfgsCfsu AD-56976 A-116407 57CfaagCfaGfaCfAfUfu 3544 A-109589 58 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asCfsaAfaAfgCf(Ayh)UfuUfgCfuUfuUfgUfL AfaacAfgGfuCfuAfgs 96 asa AD-60907 A-117428 643CfsusAfgAfcCfuGfUf 3602 A-122310 644 asCfsaAfaAfgCfa(AyUfuUfgCfuUfuUfgUfL h)aacAfgGfuCfuAfgs 96 asa AD-60908 A-117428 645CfsusAfgAfcCfuGfUf 3602 A-122311 646 asCfsaAfaAfgCfaAf(UfuUfgCfuUfuUfgUfL Ayh)acAfgGfuCfuAfg 96 sasa AD-60909 A-117428 647CfsusAfgAfcCfuGfUf 3602 A-122312 648 asCfsaAfaAfgCfaAfaUfuUfgCfuUfuUfgUfL (Ayh)cAfgGfuCfuAfg 96 sasa AD-60910 A-117428 649CfsusAfgAfcCfuGfUf 3602 A-122313 650 asCfsaAfaAfgCf(AyhUfuUfgCfuUfuUfgUfL )AfaacAf(Gyh)GfuCf 96 (Uyh)Afgsasa AD-60911 A-122307651 Cfsus(Ayh)(Gyh)(Ay 3602 A-117429 652 asCfsaAfaAfgCfaAfah)(Cyh)CfuGfUfUfuU acAfgGfuCfuAfgsasa f(G yh)Cf(Uyh)Uf(Uyh)U f(Gyh)UfL96AD-60912 A-122308 653 (Cyh)u(Ayh)(Gyh) 3602 A-117429 654asCfsaAfaAfgCfaAfa (Ayh)(Cyh)CfuGfUfU acAfgGfuCfuAfgsasafuUf(Gyh)Cf(Uyh)Uf (Uyh)Uf(Gyh)UfL96 AD-60913 A-122307 655Cfsus(Ayh)(Gyh)(Ayh) 3602 A-122309 656 asCfsaAfaAfgCf(Ayh(Cyh)CfuGfUfUfuUf(G )AfaacAfgGfuCfuAfgs yh)Cf(Uyh)Uf(Uyh)U asaf(Gyh)UfL96 AD-60914 A-122307 657 Cfsus(Ayh)(Gyh)(Ayh) 3602 A-122310 658asCfsaAfaAfgCfa(Ay (Cyh)CfuGfUfUfuUf(G h)aacAfgGfuCfuAfgsyh)Cf(Uyh)Uf(Uyh)U asa f(Gyh)UfL96 AD-60915 A-122307 659Cfsus(Ayh)(Gyh)(Ayh) 3602 A-122311 660 asCfsaAfaAfgCfaAf((Cyh)CfuGfUfUfuUf(G Ayh)acAfgGfuCfuAf yh)Cf(Uyh)Uf(Uyh)U gsasaf(Gyh)UfL96 AD- A-117428 661 CfsusAfgAfcCfuGfUf 3602 A-117429 662asCfsaAfaAfgCfaAfa 579285 UfuUfgCfuUfuUfgUfL acAfgGfuCfuAfgsasa 96AD-60916 A-122307 663 Cfsus(Ayh)(Gyh)(Ayh) 3602 A-122312 664asCfsaAfaAfgCfaAfa (Cyh)CfuGfUfUfuUf(G (Ayh)cAfgGfuCfuAfgsyh)Cf(Uyh)Uf(Uyh)U asa f(Gyh)UfL96 AD-60917 A-122307 665Cfsus(Ayh)(Gyh)(Ayh) 3602 A-122313 666 asCfsaAfaAfgCf(Ayh(Cyh)CfuGfUfUfuUf(G )AfaacAf(Gyh)GfuCf yh)Cf(Uyh)Uf(Uyh)U (Uyh)Afgsasaf(Gyh)UfL96 AD-60918 A-122308 667 (Cyh)u(Ayh)(Gyh) 3602 A-122309 668asCfsaAfaAfgCf(Ayh (Ayh)(Cyh)CfuGfUfU )AfaacAfgGfuCfuAfgsfuUf(Gyh)Cf(Uyh)Uf asa (Uyh)Uf(Gyh)UfL96 AD-60919 A-122308 669(Cyh)u(Ayh)(Gyh)(Ayh) 3602 A-122310 670 asCfsaAfaAfgCfa(Ay(Cyh)CfuGfUfUfuUf h)aacAfgGfuCfuAfgsas (Gyh)Cf(Uyh)Uf(Uyh) aUf(Gyh)UfL96 AD-60920 A-122308 671 (Cyh)u(Ayh)(Gyh)(A 3602 A-122311 672asCfsaAfaAfgCfaAf( yh)(Cyh)CfuGfUfUfu Ayh)acAfgGfuCfuAfg Uf(Gyh)Cf(Uyh)Uf(Uyh) sasa Uf(Gyh)UfL96 AD-60921 A-122308 673(Cyh)u(Ayh)(Gyh) 3602 A-122312 674 asCfsaAfaAfgCfaAfa (Ayh)(Cyh)CfuGfU(Ayh)cAfgGfuCfuAfg fUfuUf sasa (Gyh)Cf(Uyh)Uf (Uyh)Uf(Gyh)UfL96 AD-60922A-122308 675 (Cyh)u(Ayh)(Gyh) 3602 A-122313 676 asCfsaAfaAfgCf(Ayh(Ayh)(Cyh)CfuGfU )AfaacAf(Gyh)GfuCf fUfuUf (Uyh (Gyh)Cf(Uyh)Uf )Afgsasa(Uyh)Uf(Gyh)UfL96 AD-58900 677 CfsasAfgCfaGfaCfAf 3602 678asAfsaAfaGfaUfaAfa UfuUfaUfcUfuUfuUfL ugUfcUfgCfuUfgscsu 96 AD-59849A-121244 679 CfsusAfgAfcCfuGfUf 3602 680 asCfsaAfaagCfaAfaaUfuUfgcuuuuguL96 cAfgGfucuAfgsasa AD-60688 A-120188 681csusagacCfuGfuuuug 3602 682 asCfsaAfaagCfaAfaa cuuuuguL96cAfgGfucuAfgsasa AD-60212 A-122088 683 csusagacCfuGfudTuu 3602 684asCfsaAfAfAfgCfaAf gcuuuuguL96 aAfcAfgGfuCfuagsa sa

Example 2: Phase I Clinical Trial of AD-60212

A Phase I, randomized, single-blind, placebo-controlled study,including, a single ascending dose (SAD) arm and a multi-ascending dose(MAD) arm, was conducted in subjects with elevated low-densitylipoprotein cholesterol (LDLc or LDL-C), on or off statins, to evaluatethe safety, tolerability, pharmacokinetics and pharmacodynamics ofsubcutaneously administered AD-60212.

More specifically, in the SAD phase of the study, the ability of asingle subcutaneous fixed dose of 25 mg, 100 mg, 300 mg, 500 mg, or 800mg of AD-60212 (ALN-PCSsc) to lower both PCSK9 protein and LDL-C inhealthy volunteer subjects with baseline LDL-C ≥100 mg/dl (≥2.6 mmol/L)and fasting triglycerides <400 mg/dl (<4.5 mmol/L) was tested. In theMAD phase of the study, subjects with LDL-C ≥100 mg/d1, and fastingtriglycerides <400 mg/dl (<4.5 mmol/L) on and off of a stable dose ofstatin for ≥30 days prior to screening were treated with multiplesubcutaneous injections of AD-60212 to test the ability of AD-60212 tolower both PCSK9 protein and LDL-C. Subjects in the multipleadministration arm of the study were administered a single 125 mg fixeddose of AD-60212 once every week for four weeks (125 mg qW×4), or asingle 250 mg fixed dose of AD-60212 once every two weeks for one month(250 mg q2W×2), or a single 300 mg fixed dose of AD-60212 once everymonth for two months (300 mg qM×2) without statin therapy, or a single300 mg fixed dose of AD-60212 once every month for two months (300 mgqM×2) with statin therapy, or a single 500 mg fixed dose of AD-60212once every month for two months (500 mg qM×2) without statin therapy, ora single 500 mg fixed dose of AD-60212 once every month for two months(500 mg qM×2) with statin therapy.

Plasma PCSK9 protein levels were determined using an ELISA assay andserum LDL-C levels were determined directly by 0-quantification (MedpaceReference Laboratories, Leuven, Belgium). The levels of totalcholesterol, high-density lipoprotein cholesterol (HDL-C), non-HDL-C(total cholesterol minus HDL-C), apolipoprotein B, lipoprotein (a) andtriglyceride were also determined.

The cohort demographics and the baseline characteristics of the subjectsin the SAD phase of the study are provided in Table 2A and the cohortdemographics and the baseline characteristics of the subjects in the MADphase of the study are provided in Table 2B.

The unmodified sense and antisense sequences of AD-60212 are:

Sense- (SEQ ID NO: 686) 5′- CUAGACCUGUTUUGCUUUUGU-3′; and Antisense-(SEQ ID NO: 685) 5′- ACAAAAGCAAAACAGGUCUAGAA-3′

The modified sense and antisense sequences of AD-60212 are:

Sense- (SEQ ID NO: 687) 5′-csusagacCfuGfudTuugcuuuugu-3′; and Antisense-(SEQ ID NO: 688) 5′- asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′

SAD Phase

AD-60212 was well tolerated at all dose levels in the SAD phase andthere were no treatment discontinuations due to adverse events (AEs) andno serious AEs were reported.

The knockdown of PCSK9 protein levels in the single dose cohort, shownas a percent mean PCSK9 knockdown relative to baseline, is shown in FIG.1 , and the lowering of LDL-C levels in the single dose cohort, shown asa percent mean LDL-C lowering relative to baseline, is shown in FIG. 2 .Table 3 provides the mean (SD) percent change from baseline in theprotein level of PCSK9, the level of LDL-C, the level of totalcholesterol, the level of HDL-C, the level of non-HDL-C, the level ofapolipoprotein B, the level of triglycerides, and the level ofapolipoprotein a at days 84 and 180 post-dose in the SAD phase.

The data demonstrate that administration of AD-60212 reduced PCSK9levels in a dose-dependent manner up to 300 mg. Doses ≥300 mg producedsimilar, sustained reductions in PCSK9 levels that were maintained overa period of at least 6 months. PCSK9 levels returned to baseline (meanof last three measurements ≥80% of baseline) by day 180 in the 25-mg and100-mg dose cohorts. In subjects receiving doses ≥300 mg (n=12), themaximum individual relative reduction from baseline in PCSK9 levels was89% (800-mg dose, day 112). The mean maximal percent reduction (meanpercent reduction at individual nadir) was 82% and was observed in the800-mg dose cohort. Change from baseline in PCSK9 levels in subjectsreceiving ALN-PCSsc 300-800 mg (n=2-6 per dose group), was significantlygreater than in placebo-treated subjects (P<0.011) for all 11measurement points from day 7±1 post-treatment through day 112post-treatment.

The data further demonstrate that AD-60212 administration resulted indose-dependent LDL-C reductions up to 300 mg, at which near maximalreductions were achieved. LDL-C reductions were similar across the300-800 mg dose range. In subjects receiving these doses (n=12), themaximum individual decrease from baseline in LDL-C was 78% (500-mg dose;day 56). The mean maximal and maximal least-squares mean (LSM) percentreductions were 59% and were observed in the 500 and 800-mg cohorts.LDL-C levels returned towards baseline levels by 180 days after the lastadministration of the 25-mg and 100-mg doses. LDL-C reduction wasmaintained until at least day 180 after doses ≥300 mg. LDL-C reductionfrom baseline in subjects receiving ALN-PCSsc 300-800 mg (n=3-6) wasstatistically significant compared with placebo (P<0.037) in all 10determinations from day 14±2 after treatment through day 112 aftertreatment.

Decreases in total cholesterol, non-HDL-C, apolipoprotein B andlipoprotein (a) concentrations were also noted in AD-60212-treatedsubjects. Reductions in these parameters were statistically significantcompared with placebo for the majority of comparisons.

MAD Phase

AD-60212 was also well tolerated at all dose levels in the MAD phase andthere were no treatment discontinuations due to adverse events (AEs) andno serious AEs were reported.

The knockdown of PCSK9 protein levels in the multiple dose cohort, shownas a percent mean PCSK9 knockdown relative to baseline, is shown in FIG.3 , and the lowering of LDL-C levels in the multiple dose cohort, shownas a percent mean LDL-C lowering relative to baseline, is shown in FIG.4 . Table 4 provides the mean (SD) percent change from baseline in theprotein level of PCSK9, the level of LDL-C, the level of totalcholesterol, the level of HDL-C, the level of non-HDL-C, the level ofapolipoprotein B, the level of triglycerides, and the level ofapolipoprotein a at days 84 and 180 post-dose in the SAD phase.

The data demonstrate that PCSK9 protein levels were reduced followingadministration of AD-60212 with all treatment regimens studied.Reductions were similar across all multiple dose cohorts and thereductions were maintained for at least 6 months after the last dose.Consistent with published literature (Khera A V, et al. (2015) Am JCardiol 115:178-82; Guo Y L, et al. (2013) Clin Drug Investig33:877-83), baseline values of PCSK9 were higher in subjects receivingstable doses of statins. Reductions in PCSK9 were independent ofbaseline PCSK9 levels and similar in subjects irrespective of statintherapy. The maximum individual reduction from baseline in PCSK9 was 94%(500 mg QM×2 co-administered with statin, day 63). The mean maximalpercent reduction was 89%, observed in subjects receiving the 500-mgdose co-treated with a statin. Change in PCSK9 concentrations frombaseline in subjects receiving multiple doses of AD-60212 as monotherapy(i.e., without statins; n=3-6 per dose group), was significantly greaterthan placebo (P≤0.002) for all 15 measurement points from day 4post-treatment through day 126.

The data further demonstrate that similar sustained LDL-C reductionswere achieved with all multiple dose AD-60212 treatment regimens. LDL-Creduction was independent of baseline LDL-C levels and similar with andwithout statin co-therapy. The maximum individual LDL-C reduction was83% (500 mg QM×2 co-administered with statin, day 29). The mean maximalpercent reduction in LDL-C was 64% with a LSM reduction of 60% observedin the cohort receiving the 300-mg dose without statin. LDL-C loweringin all MD cohorts persisted for at least 6 months.

Change in LDL-C from baseline in AD-60212 monotherapy subjects (n=3-6)differed significantly from placebo (P≤0.05) over periods ranging from˜8 to ˜17 weeks depending on the treatment regimen.

Decreases in total cholesterol, non-HDL-C, apolipoprotein B andlipoprotein (a) concentrations were also noted in ALN-PCSsc-treatedsubjects. Reductions in these parameters were statistically significantcompared with placebo for the majority of comparisons.

In summary, subcutaneous administration of AD-60212 targeting PCSK9 toreduce LDL-C levels, was well tolerated in single doses of 25 to 800 mg,and in MD regimens of 2-4 doses totaling 500-1000 mg over a 28-dayperiod.

As shown in Figures land 2 and Table 3, a single subcutaneous injectionof a fixed dose (≥300 mg of AD-60212 resulted in durable knockdown ofPCSK9 and lowering of LDL-C for over 6 months after a single dose. Therewas up to 89% maximal PCSK9 knockdown, with a mean maximal PCSK9reduction of 82%, and up to 78% maximal reduction LDL-C lowering, with amean maximal LDL-C reduction of 59% after administration of a singlefixed dose of AD-60212. In addition, LDL-C was significantly (P<0.001)reduced by a mean of 44% at day 140 after a single dose.

As shown in FIGS. 3 and 4 and Table 4, two monthly fixed doses ofAD-60212 resulted in up to 94% maximal knockdown of PCSK9, with a meanmaximal PCSK9 reduction of 89%, and up to 83% maximal reduction ofLDL-C, with a mean maximal LDL-C reduction of 64%, with or withoutconcomitant statin administration.

These data demonstrate that single doses of AD-60212 (≥300 mg) and allmultiple doses demonstrated herein were associated with highly sustainedreductions of circulating concentrations of both PCSK9 and LDL-C. Atthese doses, the effect on PCSK9 and LDL-C remained significantlyreduced for at least 180 days post-treatment, such that PCSK9 reductionsof up to 76%, and LDL-C reductions of up to 48% were still apparent 6months after the last AD-60212 injection, and demonstrated remarkablylittle variation over the 6-month post-dose period. Additive serum LDL-Clowering was attained with AD-60212 when added to statin therapy, andthe combination therapy did not impact the safety and tolerability ofeither agent.

In both the SAD and MAD phases, decreases in total cholesterol,non-HDL-C, apolipoprotein B and lipoprotein (a) concentrations wereobserved in AD-60212-treated subjects. Reductions in these parameterswere statistically significant compared with placebo for the majority ofcomparisons.

TABLE 2A SAD Cohort Demographics and Baseline Characteristics. Singleascending dose phase ALN-PCSsc Placebo 25 mg 100 mg 300 mg 500 mg (n =6) (n = 3) (n = 3) (n = 3) (n = 3) Age, 48 (14.2) 47 (14.2) 48 (6.2) 48(12.7) 39 (14.0) years Mean (SD) Sex, n (%) Male 2 (33.3%) 3 (100%) 3(100%) 3 (100%) 3 (100%) Race, n (%) White 4 (66.7%) 2 (66.7%) 3 (100%)1 (33.3%) 3 (100%) Black or 2 (33.3%) 1 (33.3%) 0 1 (33.3%) 0 AfricanAmerican Asian 0 0 0 1 (33.3%) 0 Other 0 0 0 0 0 Body 70.6 (12.04) 84.5(2.11) 77.3 (6.66) 81.2 (11.04) 71.6 (7.93) weight, kg Mean (SD) Height,168 (10.6) 175 (2.3) 174 (5.1) 173 (9.6) 175 (3.1) cm Mean (SD) BMI,24.9 (3.17) 27.7 (0.21) 25.5 (2.10) 27.0 (1.29) 23.4 (3.01) kg/m² Mean(SD) LDL-C, 3.4 (0.50) 4.6 (1.31) 3.9 (0.92) 4.2 (0.95) 3.1 (0.44)mmol/L Mean (SD) TG, 0.8 (0.14) 1.3 (0.67) 2.0 (1.16) 1.5 (0.55) 1.8(0.95) mmol/L Mean (SD) PCSK9, 278.95 (99.53) 342.65 (67.89) 233.77(39.17) 253.82 (22.36) 263.23 (24.98) μg/L Mean (SD) Single ascendingdose phase Placebo ALN-PCSsc With 800 mg Overall Statin No Statin (n =6) (n = 24) (n = 4) (n = 8) Age, 49 (6.7) 47 (10.7) 58 (3.0) 51 (14.2)years Mean (SD) Sex, n (%) Male 5 (83.3%) 19 (79.2%) 2 (50.0%) 6 (75.0%)Race, n (%) White 3 (50.0%) 16 (66.7%) 4 (100%) 7 (87.5%) Black or 0 4(16.7%) 0 0 African American Asian 1 (16.7%) 2 (8.3%) 0 0 Other 2(33.3%) 2 (8.3%) 0 1 (12.5%) Body 74.0 (6.01) 75.5 (9.16) 74.3 (5.07)77.6 (10.31) weight, kg Mean (SD) Height, 169 (5.5) 172 (7.2) 168 (10.5)171 (9.3) cm Mean (SD) BMI, 25.9 (1.60) 25.6 (2.39) 26.5 (2.72) 26.7(2.64) kg/m² Mean (SD) LDL-C, 4.1 (0.74) 3.8 (0.85) 3.7 (2.32) 3.4(0.54) mmol/L Mean (SD) TG, 1.3 (0.24) 1.4 (0.65) 1.7 (0.53) 1.4 (0.43)mmol/L Mean (SD) PCSK9, 279.62 (66.90) 276.32 (68.28) 460.69 (56.295)276.23 (58.69) μg/L Mean (SD) BMI = body mass index; LDL-C = low-densitylipoprotein cholesterol; PCSK9 = proprotein convertase subtilisin/kexintype 9; QM × 2 = 2 monthly doses; QW × 4 = 4 weekly doses; Q2W × 2 = 2biweekly doses; SD = standard deviation; TG = triglycerides. To convertvalues for cholesterol to mg/dL multiply by 38.67. To convert values forTG to mg/dL multiply by 88.57.

TABLE 2B MAD Cohort Demographics and Baseline Characteristics. Multipledose phase ALN-PCSsc Placebo 300 mg 300 mg 500 mg With QM × 2 QMx × 2 QM× 2 Statin No Statin With Statin No Statin With Statin (n = 4) (n = 8)(n = 4) (n = 6) (n = 5) Age, years 58 (3.0) 51 (14.2) 52 (21.6) 47 (8.7)56 (11.5) Mean (SD) Sex, n (%) Male 2 (50.0%) 6 (75.0%) 2 (50.0%) 6(100%) 2 (40.0%) Race, n (%) White 4 (100%) 7 (87.5%) 3 (75.0%) 6 (100%)3 (60.0%) Black or 0 0 0 0 1 (20.0%) African American Asian 0 0 1(25.0%) 0 1 (20.0%) Other 0 1 (12.5%) 0 0 0 Body 74.3 (5.07) 77.6(10.31) 85.0 (22.04) 77.8 (15.19) 71.9 (11.03) weight, kg Mean (SD)Height, cm 168 (10.5) 171 (9.3) 176 (12.5) 175 (7.4) 167 (11.7) Mean(SD) BMI, kg/m² 26.5 (2.72) 26.7 (2.64) 27.1 (3.59) 25.2 (2.95) 25.7(1.97) Mean (SD) LDL-C, 3.7 (2.32) 3.4 (0.54) 3.7 (0.79) 3.7 (0.52) 2.7(0.51) mmol/L Mean (SD) TG, mmol/L 1.7 (0.53) 1.4 (0.43) 1.5 (0.98) 1.5(1.02) 1.1 (0.50) Mean (SD) PCSK9, μg/L 460.69 (56.295) 276.23 (58.69)460.69 (209.435) 311.47 (59.85) 433.44 (107.28) Mean (SD) Multiple dosephase ALN-PCSsc 500 mg 125 mg 250 mg QM × 2 QW × 4 Q2W × 2 No Statin NoStatin No Statin Overall (n = 6) (n = 6) (n = 6) (n = 45) Age, years 42(16.1) 55 (9.4) 61 (6.3) 52 (12.7) Mean (SD) Sex, n (%) Male 3 (50.0%) 4(66.7%) 4 (66.7%) 29 (64.4%) Race, n (%) White 5 (83.3%) 5 (83.3%) 3(50.0%) 36 (80.0%) Black or 0 0 1 (16.7%) 2 (4.4%) African AmericanAsian 1 (16.7%) 1 (16.7%) 0 4 (8.9%) Other 0 0 2 (33.3%) 3 (6.7%) Body64.9 (7.86) 73.1 (7.07) 83.2 (8.12) 75.8 (12.03) weight, kg Mean (SD)Height, cm 168 (5.3) 167 (6.9) 176 (10.1) 171 (9.2) Mean (SD) BMI, kg/m²23.0 (2.34) 26.2 (2.72) 27.0 (1.93) 25.9 (2.72) Mean (SD) LDL-C, 3.2(1.29) 3.6 (0.48) 3.8 (0.37) 3.5 (0.92) mmol/L Mean (SD) TG, mmol/L 1.0(0.23) 1.0 (0.29) 1.8 (0.78) 1.4 (0.66) Mean (SD) PCSK9, μg/L 288.07(69.07) 380.03 (50.63) 288.73 (53.53) 348.34 (103.99) Mean (SD) BMI =body mass index; LDL-C = low-density lipoprotein cholesterol; PCSK9 =proprotein convertase subtilisin/kexin type 9; QM × 2 = 2 monthly doses;QW × 4 = 4 weekly doses; Q2W × 2 = 2 biweekly doses; SD = standarddeviation; TG = triglycerides. To convert values for cholesterol tomg/dL multiply by 38.67. To convert values for TG to mg/dL multiply by88.57.

TABLE 3 Mean (SD) percent change from baseline in pharmacodynamicparameters in the SAD phase (Pharmacodynamic population) ALN-PCSscPlacebo 25 mg 100 mg 300 mg 500 mg 800 mg (n = 6) (n = 3) (n = 3) (n =3) (n = 3) (n = 6) PCSK9 Day 84 n 5 2 3 3 3 6 Mean (SD) percent change−0.1 (14.3) −47.3 (7.2) −29.9 (12.9) −72.6 (12.1) −68.7 (9.8) −72.2(8.5) Day 180 n NA NA 2 3 2 4 Mean (SD) percent change NA NA −15.7 (0.2)−47.8 (24.8) −70.3 (6.6) −74.3 (13.2) Mean (SD) percent change −29.4(9.53) −54.3 (4.75) −48.9 (27.37) −77.9 (3.49) −75.7 (11.75) −82.3(4.85) at individual nadir^(a) Mean (SD) percent change −17.5 (19.56)−51.2 (0.56) −41.7 (21.28) −74.0 (0.57) −77.7 (1.28) −79.4 (3.27) atgroup nadir^(b) Time to group nadir, days 35 42 42 42 112 98 LDL-C Day84 n 5 2 3 3 3 5 Mean (SD) percent change −7.5 (15.6) −27.9 (11.4) −36.6(6.1) −48.4 (19.0) −47.6 (15.2) −41.9 (12.3) Day 180 n NA NA 2 3 2 4Mean (SD) percent change NA NA −26.3 (2.1) −47.8 (0.5) −37.9 (21.7)−35.2 (16.8) Mean (SD) percent change −18.7 (5.61) −34.5 (8.62) −42.9(15.35) −55.0 (10.03) −55.1 (19.93) −59.2 (12.25) at individualnadir^(a) Mean (SD) percent change −8.6 (18.07) −27.9 (11.43) −38.7(2.07) −48.4 (18.99) −55.1 (24.46) −51.8 (8.44) at group nadir^(b) Timeto group nadir, days 98 84 140 84 98 35 Total cholesterol Day 84 −1.3(11.7) −20.2 (9.4) −18.2 (10.7) −30.9 (9.4) −24.2 (10.2) −28.1 (11.7)Day 180 NA NA −14.1 (2.9) −30.5 (5.7) −23.5 (11.1) −25.0 (12.2) HDL-CDay 84 11.7 (14.4) 8.3 (10.3) 19.6 (17.7) 50.5 (71.3) 6.5 (6.4) 1.9(17.0) Day 180 NA NA 18.1 (26.3) 12.8 (42.5) −2.8 (2.8) −0.2 (16.4)non-HDL-C Day 84 −6.6 (12.2) −25.5 (11.3) −28.8 (7.5) −47.2 (19.2) −34.1(12.6) −36.0 (12.6) Day 180 NA NA −21.2 (3.6) −38.0 (12.6) −29.5 (13.6)−30.4 (13.4) Apolipoprotein B Day 84 −10.0 (15.6) −18.2 (9.7) −28.1(15.6) −45.5 (20.5) −36.0 (11.7) −44.5 (11.8) Day 180 NA NA −30.5 (7.6)−37.6 (12.2) −29.2 (18.8) −27.7 (13.6) Triglycerides Day 84 −12.4 (7.9)−9.0 (19.7) −9.6 (20.2) −25.1 (29.2) 15.1 (28.1) 24.6 (48.2) Day 180 NANA −18.7 (35.5) 45.0 (105.8) −8.6 (10.1) −7.4 (23.2) Lipoprotein (a) Day84 6.7 (25.7) −2.8 (29.0) −20.1 (3.5) −33.8 (46.7) −30.4 (27.0) −22.1(20.8) Day 180 NA NA 6.6 (23.7) −37.9 (35.8) −31.1 (26.7) −2.5 (18.9)HDL-C = high-density lipoprotein cholesterol; LDL-C = low-densitylipoprotein cholesterol; NA = not applicable; PCSK9 = proproteinconvertase subtilisinikexin type 9; SD = standard deviation.^(a)Individual nadir values defined as the largest post-dose percentreduction from baseline value per subject. These values were thensummarized. ^(b)Group nadir is defined as the largest mean post-dosepercent change from baseline value during the study.

TABLE 4 Mean (SD) percent change from baseline in pharmacodynamicparameters in the MAD phase (Pharmacodynamic population) ALN-PCSsc 300mg 300 mg 500 mg 500 mg 125 mg 250 mg Placebo QM × 2 QM × 2 QM × 2 QM ×2 QW × 4 Q2W × 2 With Statin No Statin With Statin No Statin With StatinNo Statin No Statin No Statin (n = 3) (n = 8) (n = 3) (n = 6) (n = 5) (n= 6) (n = 6) (n = 6) PCSK9 84 days after last dose n 3 6 3 6 5 6 6 6Mean (SD) −0.5 (33.4) 1.3 (36.7) −78.1 (3.9) −70.6 (10.9) −82.6 (9.5)−74.2 (8.3) −75.0 (7.5) −78.0 (6.8) percent change 180 days after lastdose n NA NA 1 6 4 6 6 6 Mean (SD) NA NA −69.7 (NC) −62.6 (10.7) −75.9(10.8) −72.3 (14.3) −63.3 (14.5) −67.4 (9.9) percent change Mean (SD)−42.4 (3.76) −25.3 (20.51) −86.1 (2.06) −80.4 (4.92) −88.5 (3.67) −81.5(5.73) −83.8 (2.13) −82.7 (2.81) percent change at individual nadir^(a)Mean (SD) −21.2 (8.9) −6.1 (NC) −83.6 (4.06) −73.1 (6.31) −85.2 (1.83)−79.9 (5.35) −80.3 (4.73) −79.4 (3.83) percent change at group nadir^(b)Time to group 28 91 56 56 84 84 77 35 nadir, days LDL-C 84 days afterlast dose n 3 5 3 6 5 6 6 6 Mean (SD) 0.9 (33.3) −7.0 (11.6) −44.7(21.2) −48.8 (9.0) −38.9 (13.6) −48.5 (14.2) −41.8 (8.8) −50.0 (10.5)percent change 180 days after last dose n NA NA 1 6 4 6 6 6 Mean (SD) NANA −30.0 (NC) −44.3 (12.8) −44.2 (26.2) −45.3 (16.1) −34.5 (5.8) −42.1(16.6) percent change Mean (SD) −27.7 (13.19) −19.2 (9.68) −53.8 (19.78)−64.4 (13.22) −59.9 (18.14) −56.2 (14.59) −52.1 (4.75) −60.4 (11.02)percent change at individual nadir^(a) Mean (SD) −18.4 (17.7) −16.3 (NC)−46.7 (18.29) −55.7 (13.20) −48.9 (23.77) −51.9 (14.97) −44.8 (4.07)−54.8 (7.77) percent change at group nadir^(b) Time to group 35 105 7070 140 140 63 49 nadir, days Total cholesterol 84 days after 2.9 (25.1)−11.8 (11.3) −24.2 (13.4) −39.9 (7.4) −28.6 (16.1) −25.8 (9.3) −25.9(5.4) −32.0 (7.4) last dose 180 days after NA NA −13.9 (NA) −26.0 (6.5)−25.0 (19.6) −24.2 (12.8) −22.2 (4.7) −26.4 (13.9) last dose HDL-C 84days after 10.6 (11.8) −2.1 (15.1) 11.2 (9.4) 13.5 (15.6) 5.2 (15.9)13.1 (15.9) 7.3 (3.9) 7.0 (15.8) last dose 180 days after NA NA 20.5(NA) 7.5 (7.7) 3.8 (10.6) 6.0 (12.7) 3.5 (6.5) 10.2 (11.0) last dosenon-HDL-C 84 days after 1.3 (36.5) −15.1 (11.2) −35.2 (10.7) −55.3(12.7) −43.4 (19.1) −43.6 (11.8) −37.4 (9.6) −42.5 (9.2) last dose NA NA−25.5 (NA) −35.5 (8.0) −36.4 (22.0) −37.7 (15.4) −31.1 (4.9) −36.6(16.3) Apolipo- protein B 84 days after −6.1 (31.7) −15.3 (11.0) −36.8(9.7) −51.5 (10.7) −40.1 (14.0) −45.3 (11.9) −36.4 (10.1) −42.7 (9.9)last dose 180 days after NA NA −24.1 (NA) −35.1 (10.1) −34.9 (21.3)−37.4 (14.8) −24.4 (3.1) −36.5 (15.7) last dose Triglycerides 84 daysafter 1.5 (45.7) −8.1 (33.8) −8.8 (6.5) −39.3 (13.8) −16.6 (15.2) −0.1(24.5) −7.5 (19.0) −18.0 (12.0) last dose 180 days after NA NA −13.1(NA) 7.4 (37.3) 7.2 (23.1) 6.1 (15.8) −0.7 (28.9) 21.3 (48.7) last doseLipoprotein (a) 84 days after 3.2 (20.9) −14.7 (18.6) −17.9 (42.5) −19.4(24.9) −28.9 (28.0) −27.6 (15.6) −27.4 (8.9) −25.3 (12.9) last dose 180days after NA NA −12.2 (NA) −15.9 (26.6) −23.7 (26.4) −27.7 (23.7) −29.0(15.3) −28.9 (12.6) last dose HDL-C = high−density lipoproteincholesterol; LDL-C = low−density lipoprotein cholesterol; NA = notapplicable; NC = not calculated; PCSK9 = proprotein convertasesubtilisin/kexin type 9; QM × 2 = 2 monthly doses; QW × 4 = 4 weeklydoses; Q2Wx × 2 = 2 biweekly doses; SD = standard deviation.^(a)Individual nadir values defined as the largest post−dose percentreduction from baseline value per subject. These values were thensummarized. ^(b)Group nadir is defined as the largest mean post−dosepercent change from baseline value during the study.

1. A method of inhibiting the expression of a PCSK9 gene in a subject, comprising administering to the subject a fixed dose of about 25 mg to about 800 mg of a double-stranded ribonucleic acid (RNAi) agent, wherein the double-stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, the antisense strand comprising a region of complementarity which comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby inhibiting the expression of the PCSK9 gene in the subject.
 2. A method of decreasing the level of low density lipoprotein cholesterol (LDLc) in a subject, comprising administering to the subject a fixed dose of about 25 mg to about 800 mg of a double-stranded ribonucleic acid (RNAi) agent, wherein the double-stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, the antisense strand comprising a region of complementarity which comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby decreasing the level of LDLc in the subject.
 3. A method of treating a subject having a disorder that would benefit from reduction in PCSK9 expression, comprising administering to the subject a fixed dose of about 25 mg to about 800 mg of a double-stranded ribonucleic acid (RNAi) agent, wherein the double-stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, the antisense strand comprising a region of complementarity which comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby treating the subject having a disorder that would benefit from reduction in PCSK9 expression.
 4. A method of treating a subject having hyperlipidemia, comprising administering to the subject a fixed dose of about 25 mg to about 800 mg of a double-stranded ribonucleic acid (RNAi) agent, wherein the double-stranded RNAi agent comprises a sense strand and an antisense strand forming a double stranded region, the antisense strand comprising a region of complementarity which comprises at least 15 contiguous nucleotides differing by no more than 3 nucleotides from nucleotides 3544-3623 of the nucleotide sequence of SEQ ID NO:1, thereby treating the subject having hyperlipidemia.
 5. The method of claim 1, wherein the fixed dose is administered to the subject at an interval of once a week; once every two weeks; once a month; once a quarter; or bianually. 6.-9. (canceled)
 10. The method of claim 5, wherein the subject is administered a fixed dose of about 25 mg to about 50 mg once a week; a fixed dose of about 50 mg to about 100 mg once every two weeks; a fixed dose of about 100 mg to about 200 mg once a month; a fixed dose of about 200 mg to about 800 mg once a quarter; or a fixed dose of about 200 mg to about 800 mg biannually. 11.-18. (canceled)
 19. The method of claim 1, wherein the double stranded RNAi agent is administered to the subject subcutaneously.
 20. (canceled)
 21. (canceled)
 22. The method of claim 1, wherein the antisense strand comprises a nucleotide sequence corresponding to the unmodified sequence of any one of the nucleotide sequences provided in Table
 1. 23. The method of claim 1, wherein the antisense strand comprises the nucleotide sequence 5′-ACAAAAGCAAAACAGGUCUAGAA-3′(SEQ ID NO: 685).
 24. The method of claim 1, wherein the sense strand comprises the nucleotide sequence 5′-CUAGACCUGUTUUGCUUUUGU-3′ (SEQ ID NO: 686).
 25. The method of claim 1, wherein the double-stranded ribonucleic acid RNAi agent comprises at least one modified nucleotide.
 26. The method of claim 1, wherein substantially all of the nucleotides of the sense strand comprise a nucleotide modification; substantially all of the nucleotides of the antisense strand comprise a nucleotide modification; all of the nucleotides of the sense strand comprise a nucleotide modification; or all of the nucleotides of the antisense strand comprise a nucleotide modification. 27.-55. (canceled)
 56. The method of claim 1, wherein the subject is a human.
 57. The method of claim 3, wherein the disorder that would benefit from reduction in PCSK9 expression is hypercholesterolemia.
 58. The method of claim 4, wherein the hyperlipidemia is hypercholesterolemia. 59.-61. (canceled)
 62. The method of claim 23, wherein the sense strand comprises the nucleotide sequence of 5′-csusagacCfuGfudTuugcuuuugu-3′ (SEQ ID NO: 687) and the antisense strand comprises the nucleotide sequence of 5′-asCfsaAfAfAfgCfaAfaAfcAfgGfuCfuagsasa-3′ (SEQ ID NO: 688) (AD-60212), wherein a, g, c and u are 2′-O-methyl (2′-OMe) A, G, C, or U; Af, Gf, Cf or Uf are 2′-fluoro A, G, C or U; dT is 2′-deoxythymidine; and s is a phosphorothioate linkage.
 63. The method of claim 1, wherein the double-stranded ribonucleic acid RNAi agent further comprises a ligand.
 64. The method of claim 63, wherein the ligand is conjugated to the 3′ end of the sense strand of the double-stranded ribonucleic acid RNAi agent.
 65. The method of claim 63, wherein the ligand is an N-acetylgalactosamine (GalNAc) derivative.
 66. The method of claim 65, wherein the ligand is


67. The method of claim 65, wherein the double-stranded ribonucleic acid RNAi agent is conjugated to the ligand as shown in the following schematic

and, wherein X is O or S.
 68. The method of claim 67, wherein the X is O. 69.-72. (canceled)
 73. The method of claim 1, further comprising administering an additional therapeutic agent to the subject. 74.-76. (canceled)
 77. The method of claim 1, wherein the double stranded RNAi agent is administered to the subject as a pharmaceutical composition. 78.-82. (canceled)
 83. A kit for performing the method of claim 1, comprising a) the double stranded RNAi agent, and b) instructions for use, and c) optionally, means for administering the double stranded RNAi agent to the subject. 